diff --git a/cwl-tools/Sage-proteomics/Sage-proteomics.json b/cwl-tools/Sage-proteomics/Sage-proteomics.json deleted file mode 100644 index 964e5ea..0000000 --- a/cwl-tools/Sage-proteomics/Sage-proteomics.json +++ /dev/null @@ -1,24 +0,0 @@ -{"functions": [{ - "outputs": [{ - "format_1915": ["http://edamontology.org/format_3247"], - "data_0006": ["http://edamontology.org/data_0945"] - }], - "biotoolsID": "Sage-proteomics", - "inputs": [ - { - "format_1915": ["http://edamontology.org/format_3244"], - "data_0006": ["http://edamontology.org/data_0943"] - }, - { - "format_1915": ["http://edamontology.org/format_1929"], - "data_0006": ["http://edamontology.org/data_2976"] - } - ], - "taxonomyOperations": [ - "http://edamontology.org/operation_3631", - "http://edamontology.org/operation_3633", - "http://edamontology.org/operation_2428" - ], - "label": "Sage", - "id": "Sage-proteomics" -}]} \ No newline at end of file diff --git a/cwl-tools/Sage-proteomics/tool.json b/cwl-tools/Sage-proteomics/tool.json new file mode 100644 index 0000000..59f760b --- /dev/null +++ b/cwl-tools/Sage-proteomics/tool.json @@ -0,0 +1,28 @@ +[ + { + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3247"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "biotoolsID": "Sage-proteomics", + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3244"], + "data_0006": ["http://edamontology.org/data_0943"] + }, + { + "format_1915": ["http://edamontology.org/format_1929"], + "data_0006": ["http://edamontology.org/data_2976"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_3631", + "http://edamontology.org/operation_3633", + "http://edamontology.org/operation_2428" + ], + "label": "Sage", + "id": "Sage-proteomics" + } +] diff --git a/cwl-tools/XTandem/XTandem.sh b/cwl-tools/XTandem/XTandem.sh deleted file mode 100644 index 0746005..0000000 --- a/cwl-tools/XTandem/XTandem.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash -set -e - -mkdir /tmp/XTandem && \ -wget -O /tmp/XTandem/tandem.params https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/XTandem/tandem.params && \ -wget -O /tmp/XTandem/taxonomy.xml https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/XTandem/taxonomy.xml && \ -cp /data/inputs/up00000062.fasta /tmp/XTandem/fastaFile.fasta && \ -cp /data/inputs/2021-10-8_Ecoli.mzML /tmp/XTandem/mzmlFile.mzML && \ -/usr/local/tpp/bin/tandem /tmp/XTandem/tandem.params && \ -/usr/local/tpp/bin/Tandem2XML /tmp/XTandem/tandemFile.tandem > output.pep.xml \ No newline at end of file diff --git a/cwl-tools/Comet/Comet.cwl b/cwl-tools/comet/comet.cwl similarity index 95% rename from cwl-tools/Comet/Comet.cwl rename to cwl-tools/comet/comet.cwl index 729cd22..e0e6c4d 100644 --- a/cwl-tools/Comet/Comet.cwl +++ b/cwl-tools/comet/comet.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: comet label: comet-ms @@ -21,7 +21,7 @@ inputs: separate: false default: class: File - location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/Comet/comet.params + location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/comet/comet.params Comet_in_1: type: File format: "http://edamontology.org/format_3244" # mzML diff --git a/cwl-tools/Comet/comet.params b/cwl-tools/comet/comet.params similarity index 100% rename from cwl-tools/Comet/comet.params rename to cwl-tools/comet/comet.params diff --git a/cwl-tools/comet/tool.json b/cwl-tools/comet/tool.json new file mode 100644 index 0000000..a164b83 --- /dev/null +++ b/cwl-tools/comet/tool.json @@ -0,0 +1,38 @@ +[{ + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_3247"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_3475"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "inputs": [ + { + "format_1915": [ + "http://edamontology.org/format_3244", + "http://edamontology.org/format_3654", + "http://edamontology.org/format_3651" + ], + "data_0006": ["http://edamontology.org/data_0943"] + }, + { + "format_1915": ["http://edamontology.org/format_1929"], + "data_0006": ["http://edamontology.org/data_2976"] + } + ], + "taxonomyOperations": ["http://edamontology.org/operation_3646"], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl" + }, + "biotoolsID": "comet", + "label": "Comet", + "id": "Comet" + }] \ No newline at end of file diff --git a/cwl-tools/GOEnrichment/GOEnrichment.cwl b/cwl-tools/goenrichment/goenrichment.cwl similarity index 100% rename from cwl-tools/GOEnrichment/GOEnrichment.cwl rename to cwl-tools/goenrichment/goenrichment.cwl diff --git a/cwl-tools/goenrichment/tool.json b/cwl-tools/goenrichment/tool.json new file mode 100644 index 0000000..51a43c8 --- /dev/null +++ b/cwl-tools/goenrichment/tool.json @@ -0,0 +1,36 @@ +{ + "outputs": [ + { + "format_1915": [ + "http://edamontology.org/format_3603", + "http://edamontology.org/format_2330" + ], + "data_0006": ["http://edamontology.org/data_3754"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_2330"], + "data_0006": ["http://edamontology.org/data_2872"] + }, + { + "format_1915": [ + "http://edamontology.org/format_2196", + "http://edamontology.org/format_2197" + ], + "data_0006": ["http://edamontology.org/data_0582"] + }, + { + "format_1915": ["http://edamontology.org/format_3475"], + "data_0006": ["http://edamontology.org/data_0916"] + } + ], + "taxonomyOperations": ["http://edamontology.org/operation_2436"], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/goenrichment/goenrichment.cwl" + }, + "biotoolsID": "goenrichment", + "label": "GOEnrichment", + "id": "GOEnrichment" + } \ No newline at end of file diff --git a/cwl-tools/gProfiler/gProfiler.sh b/cwl-tools/gprofiler/gProfiler.sh similarity index 100% rename from cwl-tools/gProfiler/gProfiler.sh rename to cwl-tools/gprofiler/gProfiler.sh diff --git a/cwl-tools/gProfiler/gProfiler.cwl b/cwl-tools/gprofiler/gprofiler.cwl similarity index 90% rename from cwl-tools/gProfiler/gProfiler.cwl rename to cwl-tools/gprofiler/gprofiler.cwl index d4b891c..15fc2bb 100644 --- a/cwl-tools/gProfiler/gProfiler.cwl +++ b/cwl-tools/gprofiler/gprofiler.cwl @@ -1,6 +1,7 @@ cwlVersion: v1.0 class: CommandLineTool baseCommand: ["bash"] +label: gprofiler requirements: ShellCommandRequirement: {} InitialWorkDirRequirement: @@ -15,7 +16,7 @@ inputs: position: 1 default: class: File - location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/gProfiler/gProfiler.sh + location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/gprofiler/gprofiler.sh gProfiler_in_1: type: File doc: "Input file containing gene/query data" diff --git a/cwl-tools/gprofiler/tool.json b/cwl-tools/gprofiler/tool.json new file mode 100644 index 0000000..b372d41 --- /dev/null +++ b/cwl-tools/gprofiler/tool.json @@ -0,0 +1,31 @@ +{ + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3464"], + "data_0006": [ + "http://edamontology.org/data_3753", + "http://edamontology.org/data_3754", + "http://edamontology.org/data_3953" + ] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_2330"], + "data_0006": ["http://edamontology.org/data_2872"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_2422", + "http://edamontology.org/operation_3501", + "http://edamontology.org/operation_2497", + "http://edamontology.org/operation_3672" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/gprofiler/gprofiler.cwl" + }, + "biotoolsID": "gprofiler", + "label": "gProfiler", + "id": "gProfiler" + } \ No newline at end of file diff --git a/cwl-tools/idconvert/idconvert_to_mzIdentML.cwl b/cwl-tools/idconvert/idconvert_to_mzIdentML.cwl index e3e7e22..79d3dc7 100644 --- a/cwl-tools/idconvert/idconvert_to_mzIdentML.cwl +++ b/cwl-tools/idconvert/idconvert_to_mzIdentML.cwl @@ -2,7 +2,7 @@ cwlVersion: v1.0 class: CommandLineTool -label: idconvert.cwl +label: idconvert baseCommand: "/usr/local/tpp/bin/idconvert" requirements: diff --git a/cwl-tools/idconvert/idconvert_to_pepXML.cwl b/cwl-tools/idconvert/idconvert_to_pepXML.cwl index 26bc1aa..c9dc953 100644 --- a/cwl-tools/idconvert/idconvert_to_pepXML.cwl +++ b/cwl-tools/idconvert/idconvert_to_pepXML.cwl @@ -2,7 +2,7 @@ cwlVersion: v1.0 class: CommandLineTool -label: idconvert.cwl +label: idconvert baseCommand: "/usr/local/tpp/bin/idconvert" arguments: diff --git a/cwl-tools/idconvert/tool.json b/cwl-tools/idconvert/tool.json new file mode 100644 index 0000000..33b243b --- /dev/null +++ b/cwl-tools/idconvert/tool.json @@ -0,0 +1,53 @@ +[{ + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3247"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_0335", + "http://edamontology.org/operation_1812", + "http://edamontology.org/operation_3434" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/idconvert/idconvert_to_pepXML.cwl" + }, + "biotoolsID": "idconvert", + "label": "idconvert", + "id": "idconvert_to_pepXML" + }, + { + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3247"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_0335", + "http://edamontology.org/operation_1812", + "http://edamontology.org/operation_3434" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/idconvert/idconvert_to_mzIdentML.cwl" + }, + "biotoolsID": "idconvert", + "label": "idconvert", + "id": "idconvert_to_mzIdentML" + } +] \ No newline at end of file diff --git a/cwl-tools/MS_Amanda/docker/Dockerfile b/cwl-tools/ms_amanda/docker/Dockerfile similarity index 100% rename from cwl-tools/MS_Amanda/docker/Dockerfile rename to cwl-tools/ms_amanda/docker/Dockerfile diff --git a/cwl-tools/MS_Amanda/docker/build.sh b/cwl-tools/ms_amanda/docker/build.sh similarity index 100% rename from cwl-tools/MS_Amanda/docker/build.sh rename to cwl-tools/ms_amanda/docker/build.sh diff --git a/cwl-tools/MS_Amanda/MS_Amanda.cwl b/cwl-tools/ms_amanda/ms_amanda.cwl similarity index 100% rename from cwl-tools/MS_Amanda/MS_Amanda.cwl rename to cwl-tools/ms_amanda/ms_amanda.cwl diff --git a/cwl-tools/ms_amanda/tool.json b/cwl-tools/ms_amanda/tool.json new file mode 100644 index 0000000..431e729 --- /dev/null +++ b/cwl-tools/ms_amanda/tool.json @@ -0,0 +1,35 @@ +{ + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3247"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "inputs": [ + { + "format_1915": [ + "http://edamontology.org/format_3244", + "http://edamontology.org/format_3651" + ], + "data_0006": ["http://edamontology.org/data_0943"] + }, + { + "format_1915": ["http://edamontology.org/format_1929"], + "data_0006": ["http://edamontology.org/data_2976"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_2945", + "http://edamontology.org/operation_2945", + "http://edamontology.org/operation_3767", + "http://edamontology.org/operation_3645", + "http://edamontology.org/operation_3755" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ms_amanda/ms_amanda.cwl" + }, + "biotoolsID": "ms_amanda", + "label": "MS_Amanda", + "id": "MS_Amanda" + } \ No newline at end of file diff --git a/cwl-tools/MSFragger/fragger.params b/cwl-tools/msfragger/fragger.params similarity index 100% rename from cwl-tools/MSFragger/fragger.params rename to cwl-tools/msfragger/fragger.params diff --git a/cwl-tools/MSFragger/MSFragger.cwl b/cwl-tools/msfragger/msfragger.cwl similarity index 95% rename from cwl-tools/MSFragger/MSFragger.cwl rename to cwl-tools/msfragger/msfragger.cwl index ce98b1f..89837c3 100644 --- a/cwl-tools/MSFragger/MSFragger.cwl +++ b/cwl-tools/msfragger/msfragger.cwl @@ -22,7 +22,7 @@ inputs: type: File default: class: File - location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/MSFragger/fragger.params + location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/msfragger/fragger.params MSFragger_in_1: type: File format: "http://edamontology.org/format_3244" # mzML diff --git a/cwl-tools/msfragger/tool.json b/cwl-tools/msfragger/tool.json new file mode 100644 index 0000000..d8e29dd --- /dev/null +++ b/cwl-tools/msfragger/tool.json @@ -0,0 +1,33 @@ +{ + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "inputs": [ + { + "format_1915": [ + "http://edamontology.org/format_3244", + "http://edamontology.org/format_3654", + "http://edamontology.org/format_3651" + ], + "data_0006": ["http://edamontology.org/data_0943"] + }, + { + "format_1915": ["http://edamontology.org/format_1929"], + "data_0006": ["http://edamontology.org/data_2976"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_2421", + "http://edamontology.org/operation_3801" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/msfragger/msfragger.cwl" + }, + "biotoolsID": "msfragger", + "label": "MSFragger", + "id": "MSFragger" + } \ No newline at end of file diff --git a/cwl-tools/mzRecal/mzRecal.cwl b/cwl-tools/mzrecal/mzrecal.cwl similarity index 97% rename from cwl-tools/mzRecal/mzRecal.cwl rename to cwl-tools/mzrecal/mzrecal.cwl index a10b83b..de4d7c6 100644 --- a/cwl-tools/mzRecal/mzRecal.cwl +++ b/cwl-tools/mzrecal/mzrecal.cwl @@ -2,7 +2,7 @@ cwlVersion: v1.0 class: CommandLineTool -label: mzRecal.cwl +label: mzrecal requirements: DockerRequirement: dockerPull: workflomics/mzrecal:1.1.3 diff --git a/cwl-tools/mzrecal/tool.json b/cwl-tools/mzrecal/tool.json new file mode 100644 index 0000000..3b27290 --- /dev/null +++ b/cwl-tools/mzrecal/tool.json @@ -0,0 +1,28 @@ +[ + { + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3244"], + "data_0006": ["http://edamontology.org/data_0943"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3244"], + "data_0006": ["http://edamontology.org/data_0943"] + }, + { + "format_1915": ["http://edamontology.org/format_3247"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "taxonomyOperations": ["http://edamontology.org/operation_3627"], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzrecal/mzrecal.cwl" + }, + "biotoolsID": "mzrecal", + "label": "mzRecal", + "id": "mzrecal" + } +] diff --git a/cwl-tools/PeptideProphet/PeptideProphet.cwl b/cwl-tools/peptideprophet/peptideprophet.cwl similarity index 96% rename from cwl-tools/PeptideProphet/PeptideProphet.cwl rename to cwl-tools/peptideprophet/peptideprophet.cwl index 2375fe0..7abf9ae 100644 --- a/cwl-tools/PeptideProphet/PeptideProphet.cwl +++ b/cwl-tools/peptideprophet/peptideprophet.cwl @@ -1,7 +1,7 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: ["xinteract", "-Noutput_interact.pep.xml" , "-p0.95" , "-l7" , "-PPM"] -label: PeptideProphet.cwl +label: peptideprophet requirements: DockerRequirement: dockerPull: spctools/tpp:version6.3.3 diff --git a/cwl-tools/peptideprophet/tool.json b/cwl-tools/peptideprophet/tool.json new file mode 100644 index 0000000..0f2d7f0 --- /dev/null +++ b/cwl-tools/peptideprophet/tool.json @@ -0,0 +1,41 @@ +[ + { + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_2331"], + "data_0006": ["http://edamontology.org/data_2048"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_3244"], + "data_0006": ["http://edamontology.org/data_0943"] + }, + { + "format_1915": ["http://edamontology.org/format_1929"], + "data_0006": ["http://edamontology.org/data_2976"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_3664", + "http://edamontology.org/operation_3675", + "http://edamontology.org/operation_3631", + "http://edamontology.org/operation_3649" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl" + }, + "biotoolsID": "peptideprophet", + "label": "PeptideProphet", + "id": "PeptideProphet" + } +] diff --git a/cwl-tools/protXml2IdList/tool.json b/cwl-tools/protXml2IdList/tool.json new file mode 100644 index 0000000..747688b --- /dev/null +++ b/cwl-tools/protXml2IdList/tool.json @@ -0,0 +1,25 @@ +{ + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_2330"], + "data_0006": ["http://edamontology.org/data_2872"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3747"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_3434", + "http://edamontology.org/operation_0335" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/protXml2IdList/protXml2IdList.cwl" + }, + "biotoolsID": "", + "label": "protXml2IdList", + "id": "protXml2IdList" + } \ No newline at end of file diff --git a/cwl-tools/ProteinProphet/ProteinProphet.cwl b/cwl-tools/proteinprophet/proteinprophet.cwl similarity index 96% rename from cwl-tools/ProteinProphet/ProteinProphet.cwl rename to cwl-tools/proteinprophet/proteinprophet.cwl index 7cc556e..bda71ba 100644 --- a/cwl-tools/ProteinProphet/ProteinProphet.cwl +++ b/cwl-tools/proteinprophet/proteinprophet.cwl @@ -1,7 +1,7 @@ -cwlVersion: v1.0 +cwlVersion: v1.2 class: CommandLineTool baseCommand: "ProteinProphet" -label: ProteinProphet.cwl +label: proteinprophet requirements: DockerRequirement: dockerPull: spctools/tpp:version6.3.3 diff --git a/cwl-tools/proteinprophet/tool.json b/cwl-tools/proteinprophet/tool.json new file mode 100644 index 0000000..d0a8022 --- /dev/null +++ b/cwl-tools/proteinprophet/tool.json @@ -0,0 +1,38 @@ +[ + { + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3747"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_3475"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_1929"], + "data_0006": ["http://edamontology.org/data_2976"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_3664", + "http://edamontology.org/operation_3767", + "http://edamontology.org/operation_3648", + "http://edamontology.org/operation_3644", + "http://edamontology.org/operation_3695" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl" + }, + "biotoolsID": "proteinprophet", + "label": "ProteinProphet", + "id": "ProteinProphet" + } +] diff --git a/cwl-tools/StPeter/StPeter.cwl b/cwl-tools/stpeter/stpeter.cwl similarity index 97% rename from cwl-tools/StPeter/StPeter.cwl rename to cwl-tools/stpeter/stpeter.cwl index 11e4f2b..bd560a3 100644 --- a/cwl-tools/StPeter/StPeter.cwl +++ b/cwl-tools/stpeter/stpeter.cwl @@ -1,7 +1,7 @@ cwlVersion: v1.0 class: CommandLineTool baseCommand: "StPeter" -label: StPeter.cwl +label: stpeter requirements: DockerRequirement: dockerPull: spctools/tpp:version6.3.3 diff --git a/cwl-tools/stpeter/tool.json b/cwl-tools/stpeter/tool.json new file mode 100644 index 0000000..06c95b4 --- /dev/null +++ b/cwl-tools/stpeter/tool.json @@ -0,0 +1,37 @@ +[ + { + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3747"], + "data_0006": ["http://edamontology.org/data_0896"] + } + ], + "inputs": [ + { + "format_1915": ["http://edamontology.org/format_3747"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + }, + { + "format_1915": ["http://edamontology.org/format_3244"], + "data_0006": ["http://edamontology.org/data_0943"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_3637", + "http://edamontology.org/operation_3799", + "http://edamontology.org/operation_3630", + "http://edamontology.org/operation_3634" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/stpeter/stpeter.cwl" + }, + "biotoolsID": "stpeter", + "label": "StPeter", + "id": "StPeter" + } +] diff --git a/cwl-tools/xtandem/XTandem.sh b/cwl-tools/xtandem/XTandem.sh new file mode 100644 index 0000000..a5fc50a --- /dev/null +++ b/cwl-tools/xtandem/XTandem.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -e + +mkdir /tmp/xtandem && \ +wget -O /tmp/xtandem/tandem.params https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/xtandem/tandem.params && \ +wget -O /tmp/xtandem/taxonomy.xml https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/xtandem/taxonomy.xml && \ +cp /data/inputs/up00000062.fasta /tmp/xtandem/fastaFile.fasta && \ +cp /data/inputs/2021-10-8_Ecoli.mzML /tmp/xtandem/mzmlFile.mzML && \ +/usr/local/tpp/bin/tandem /tmp/xtandem/tandem.params && \ +/usr/local/tpp/bin/Tandem2XML /tmp/xtandem/tandemFile.tandem > output.pep.xml \ No newline at end of file diff --git a/cwl-tools/XTandem/tandem.params b/cwl-tools/xtandem/tandem.params similarity index 97% rename from cwl-tools/XTandem/tandem.params rename to cwl-tools/xtandem/tandem.params index 8330804..69dd746 100644 --- a/cwl-tools/XTandem/tandem.params +++ b/cwl-tools/xtandem/tandem.params @@ -1,10 +1,10 @@ - /tmp/XTandem/taxonomy.xml + /tmp/xtandem/taxonomy.xml mydatabase - /tmp/XTandem/mzmlFile.mzML - /tmp/XTandem/tandemFile.tandem + /tmp/xtandem/mzmlFile.mzML + /tmp/xtandem/tandemFile.tandem diff --git a/cwl-tools/XTandem/taxonomy.xml b/cwl-tools/xtandem/taxonomy.xml similarity index 62% rename from cwl-tools/XTandem/taxonomy.xml rename to cwl-tools/xtandem/taxonomy.xml index 5c98868..04116eb 100644 --- a/cwl-tools/XTandem/taxonomy.xml +++ b/cwl-tools/xtandem/taxonomy.xml @@ -1,6 +1,6 @@ - + diff --git a/cwl-tools/xtandem/tool.json b/cwl-tools/xtandem/tool.json new file mode 100644 index 0000000..47ead35 --- /dev/null +++ b/cwl-tools/xtandem/tool.json @@ -0,0 +1,40 @@ +{ + "outputs": [ + { + "format_1915": ["http://edamontology.org/format_3655"], + "data_0006": ["http://edamontology.org/data_0945"] + } + ], + "inputs": [ + { + "format_1915": [ + "http://edamontology.org/format_3652", + "http://edamontology.org/format_3653", + "http://edamontology.org/format_3654", + "http://edamontology.org/format_3834", + "http://edamontology.org/format_3651", + "http://edamontology.org/format_3711", + "http://edamontology.org/format_3244" + ], + "data_0006": ["http://edamontology.org/data_0943"] + }, + { + "format_1915": ["http://edamontology.org/format_1929"], + "data_0006": ["http://edamontology.org/data_2976"] + } + ], + "taxonomyOperations": [ + "http://edamontology.org/operation_3647", + "http://edamontology.org/operation_3645", + "http://edamontology.org/operation_3631", + "http://edamontology.org/operation_3646", + "http://edamontology.org/operation_3767" + ], + + "implementation": { + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/xtandem/xtandem.cwl" + }, + "biotoolsID": "xtandem", + "label": "XTandem", + "id": "XTandem" + } \ No newline at end of file diff --git a/cwl-tools/XTandem/XTandem.cwl b/cwl-tools/xtandem/xtandem.cwl similarity index 79% rename from cwl-tools/XTandem/XTandem.cwl rename to cwl-tools/xtandem/xtandem.cwl index 7b309b4..a09a3d8 100644 --- a/cwl-tools/XTandem/XTandem.cwl +++ b/cwl-tools/xtandem/xtandem.cwl @@ -3,7 +3,7 @@ cwlVersion: v1.0 class: CommandLineTool label: XTandem.cwl -baseCommand: ["mkdir", "-p", "/tmp/XTandem"] +baseCommand: ["mkdir", "-p", "/tmp/xtandem"] requirements: ShellCommandRequirement: {} DockerRequirement: @@ -19,9 +19,9 @@ requirements: - entryname: fastaFile.fasta entry: $(inputs.XTandem_in_2) arguments: - - valueFrom: "&& cp tandem.params taxonomy.xml mzmlFile.mzML fastaFile.fasta /tmp/XTandem && \ - tandem /tmp/XTandem/tandem.params && \ - Tandem2XML /tmp/XTandem/tandemFile.tandem > mzmlFile.pep.xml" + - valueFrom: "&& cp tandem.params taxonomy.xml mzmlFile.mzML fastaFile.fasta /tmp/xtandem && \ + tandem /tmp/xtandem/tandem.params && \ + Tandem2XML /tmp/xtandem/tandemFile.tandem > mzmlFile.pep.xml" position: 1 shellQuote: false inputs: @@ -29,12 +29,12 @@ inputs: type: File default: class: File - location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/docker/cwl/tools/XTandem/tandem.params + location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/docker/cwl/tools/xtandem/tandem.params Taxonomy: type: File default: class: File - location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/docker/cwl/tools/XTandem/taxonomy.xml + location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/docker/cwl/tools/xtandem/taxonomy.xml XTandem_in_1: type: File diff --git a/domains/proteomics/tools.json b/domains/proteomics/tools.json index dc42f17..5c28955 100644 --- a/domains/proteomics/tools.json +++ b/domains/proteomics/tools.json @@ -32,7 +32,7 @@ "taxonomyOperations": ["http://edamontology.org/operation_3646"], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl" }, "biotoolsID": "comet", "label": "Comet", @@ -71,7 +71,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl" }, "biotoolsID": "peptideprophet", "label": "PeptideProphet", @@ -107,7 +107,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl" }, "biotoolsID": "proteinprophet", "label": "ProteinProphet", @@ -142,7 +142,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/StPeter/StPeter.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/stpeter/stpeter.cwl" }, "biotoolsID": "stpeter", "label": "StPeter", @@ -168,7 +168,7 @@ "taxonomyOperations": ["http://edamontology.org/operation_3627"], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzRecal/mzRecal.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzrecal/mzrecal.cwl" }, "biotoolsID": "mzrecal", "label": "mzRecal", @@ -256,7 +256,7 @@ "taxonomyOperations": ["http://edamontology.org/operation_2436"], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/GOEnrichment/GOEnrichment.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/goenrichment/goenrichment.cwl" }, "biotoolsID": "goenrichment", "label": "GOEnrichment", @@ -287,7 +287,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/gProfiler/gProfiler.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/gprofiler/gprofiler.cwl" }, "biotoolsID": "gprofiler", "label": "gProfiler", @@ -327,7 +327,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/XTandem/XTandem.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/xtandem/xtandem.cwl" }, "biotoolsID": "xtandem", "label": "XTandem", @@ -387,7 +387,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/MS_Amanda/MS_Amanda.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ms_amanda/ms_amanda.cwl" }, "biotoolsID": "ms_amanda", "label": "MS_Amanda", @@ -420,7 +420,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/MSFragger/MSFragger.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/msfragger/msfragger.cwl" }, "biotoolsID": "msfragger", "label": "MSFragger", diff --git a/domains/template-domain/tools.json b/domains/template-domain/tools.json index 5334cdb..176493b 100644 --- a/domains/template-domain/tools.json +++ b/domains/template-domain/tools.json @@ -32,7 +32,7 @@ "taxonomyOperations": ["http://edamontology.org/operation_3646"], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl" }, "biotoolsID": "comet", "label": "Comet", @@ -71,7 +71,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl" }, "biotoolsID": "peptideprophet", "label": "PeptideProphet", @@ -107,7 +107,7 @@ ], "implementation": { - "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl" + "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl" }, "biotoolsID": "proteinprophet", "label": "ProteinProphet", diff --git a/examples/cwl-workflows/example1/workflow_1.cwl b/examples/cwl-workflows/example1/workflow_1.cwl index f53c60b..601e421 100644 --- a/examples/cwl-workflows/example1/workflow_1.cwl +++ b/examples/cwl-workflows/example1/workflow_1.cwl @@ -15,20 +15,20 @@ inputs: format: "http://edamontology.org/format_1929" # FASTA steps: Comet_01: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: input_1 Comet_in_2: input_2 out: [Comet_out_1, Comet_out_2, Comet_out_3] PeptideProphet_02: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: Comet_01/Comet_out_1 PeptideProphet_in_2: input_1 PeptideProphet_in_3: input_2 out: [PeptideProphet_out_1, PeptideProphet_out_2] ProteinProphet_03: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet_02/PeptideProphet_out_1 ProteinProphet_in_2: input_2 diff --git a/examples/cwl-workflows/example2/workflow_2.cwl b/examples/cwl-workflows/example2/workflow_2.cwl index 05fd14c..9e7069e 100644 --- a/examples/cwl-workflows/example2/workflow_2.cwl +++ b/examples/cwl-workflows/example2/workflow_2.cwl @@ -15,13 +15,13 @@ inputs: format: "http://edamontology.org/format_1929" # FASTA steps: Comet1: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: input1 Comet_in_2: input2 out: [Comet_out_1] PeptideProphet2: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: Comet1/Comet_out_1 # Manual edit: PeptideProphet_in_2: input1 @@ -30,14 +30,14 @@ steps: PeptideProphet_in_3: input2 out: [PeptideProphet_out_1] ProteinProphet3: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet2/PeptideProphet_out_1 # Manual edit: ProteinProphet_in_2: input2 (FASTA) ProteinProphet_in_2: input2 out: [ProteinProphet_out_1, ProteinProphet_out_2] StPeter4: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/StPeter/StPeter.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/stpeter/stpeter.cwl in: #StPeter_in_1: ProteinProphet3/ProteinProphet_out_1 StPeter_in_1: ProteinProphet3/ProteinProphet_out_1 diff --git a/examples/cwl-workflows/example3/workflow_3.cwl b/examples/cwl-workflows/example3/workflow_3.cwl index 89686b0..795fe15 100644 --- a/examples/cwl-workflows/example3/workflow_3.cwl +++ b/examples/cwl-workflows/example3/workflow_3.cwl @@ -15,13 +15,13 @@ inputs: format: "http://edamontology.org/format_1929" # FASTA steps: Comet1: - run: ../..//tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: input1 Comet_in_2: input2 out: [Comet_out_1] PeptideProphet2: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: Comet1/Comet_out_1 # Manual edit: PeptideProphet_in_2: input1 @@ -30,7 +30,7 @@ steps: PeptideProphet_in_3: input2 out: [PeptideProphet_out_1] ProteinProphet3: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet2/PeptideProphet_out_1 # Manual edit: ProteinProphet_in_2: input2 (FASTA) diff --git a/examples/cwl-workflows/example4/workflow_4.cwl b/examples/cwl-workflows/example4/workflow_4.cwl index 814fc6a..179da54 100644 --- a/examples/cwl-workflows/example4/workflow_4.cwl +++ b/examples/cwl-workflows/example4/workflow_4.cwl @@ -15,7 +15,7 @@ inputs: format: "http://edamontology.org/format_1929" # FASTA steps: Comet1: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: input1 Comet_in_2: input2 @@ -27,19 +27,19 @@ steps: idconvert_in_1: Comet1/Comet_out_1 out: [idconvert_out_1] mzRecal3: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzRecal/mzRecal.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzrecal/mzrecal.cwl in: mzRecal_in_1: input1 mzRecal_in_2: idconvert2/idconvert_out_1 out: [mzRecal_out_1] Comet4: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: mzRecal3/mzRecal_out_1 Comet_in_2: input2 out: [Comet_out_1] PeptideProphet5: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: Comet4/Comet_out_1 # Manual edit: PeptideProphet_in_2: mzRecal3/mzRecal_out_1 @@ -49,7 +49,7 @@ steps: out: [PeptideProphet_out_1] ProteinProphet6: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet5/PeptideProphet_out_1 # Manual edit: ProteinProphet_in_2: input2 diff --git a/examples/cwl-workflows/example5/workflow_5.cwl b/examples/cwl-workflows/example5/workflow_5.cwl index f2dd0c6..e24bd44 100644 --- a/examples/cwl-workflows/example5/workflow_5.cwl +++ b/examples/cwl-workflows/example5/workflow_5.cwl @@ -21,7 +21,7 @@ inputs: format: "http://edamontology.org/format_3475" # TSV steps: Comet1: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: input1 Comet_in_2: input2 @@ -33,19 +33,19 @@ steps: idconvert_in_1: Comet1/Comet_out_1 out: [idconvert_out_1] mzRecal3: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzRecal/mzRecal.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzrecal/mzrecal.cwl in: mzRecal_in_1: input1 mzRecal_in_2: idconvert2/idconvert_out_1 out: [mzRecal_out_1] Comet4: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: mzRecal3/mzRecal_out_1 Comet_in_2: input2 out: [Comet_out_1] PeptideProphet5: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: Comet4/Comet_out_1 # Manual edit: PeptideProphet_in_2: mzRecal3/mzRecal_out_1 @@ -54,7 +54,7 @@ steps: PeptideProphet_in_3: input2 out: [PeptideProphet_out_1] ProteinProphet6: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet5/PeptideProphet_out_1 # Manual edit: ProteinProphet_in_2: input2 @@ -66,7 +66,7 @@ steps: protXml2IdList_in_1: ProteinProphet6/ProteinProphet_out_1 out: [protXml2IdList_out_1] GOEnrichment8: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/GOEnrichment/GOEnrichment.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/goenrichment/goenrichment.cwl in: GOEnrichment_in_1: protXml2IdList7/protXml2IdList_out_1 GOEnrichment_in_2: input3 diff --git a/examples/cwl-workflows/example6/workflow_6.cwl b/examples/cwl-workflows/example6/workflow_6.cwl index 6e237c0..c343339 100644 --- a/examples/cwl-workflows/example6/workflow_6.cwl +++ b/examples/cwl-workflows/example6/workflow_6.cwl @@ -15,25 +15,25 @@ inputs: format: "http://edamontology.org/format_1929" # FASTA steps: XTandem1: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/XTandem/XTandem.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/xtandem/xtandem.cwl in: XTandem_in_1: input1 XTandem_in_2: input2 out: [XTandem_out_1] mzRecal2: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzRecal/mzRecal.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzrecal/mzrecal.cwl in: mzRecal_in_1: input1 mzRecal_in_2: XTandem1/XTandem_out_1 out: [mzRecal_out_1] Comet3: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: mzRecal2/mzRecal_out_1 Comet_in_2: input2 out: [Comet_out_1] PeptideProphet4: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: Comet3/Comet_out_1 # Manual edit: PeptideProphet_in_2: mzRecal3/mzRecal_out_1 @@ -42,7 +42,7 @@ steps: PeptideProphet_in_3: input2 out: [PeptideProphet_out_1] ProteinProphet5: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet4/PeptideProphet_out_1 # Manual edit: ProteinProphet_in_2: input2 @@ -54,7 +54,7 @@ steps: protXml2IdList_in_1: ProteinProphet5/ProteinProphet_out_1 out: [protXml2IdList_out_1] gProfiler7: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/gProfiler/gProfiler.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/gprofiler/gprofiler.cwl in: gProfiler_in_1: protXml2IdList6/protXml2IdList_out_1 out: [gProfiler_out_1] diff --git a/examples/cwl-workflows/example7/workflow_7.cwl b/examples/cwl-workflows/example7/workflow_7.cwl index ccfcaf5..f29e97d 100644 --- a/examples/cwl-workflows/example7/workflow_7.cwl +++ b/examples/cwl-workflows/example7/workflow_7.cwl @@ -15,25 +15,25 @@ inputs: format: "http://edamontology.org/format_1929" # FASTA steps: XTandem1: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/XTandem/XTandem.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/xtandem/xtandem.cwl in: XTandem_in_1: input1 XTandem_in_2: input2 out: [XTandem_out_1] mzRecal2: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzRecal/mzRecal.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/mzrecal/mzrecal.cwl in: mzRecal_in_1: input1 mzRecal_in_2: XTandem1/XTandem_out_1 out: [mzRecal_out_1] Comet3: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/Comet/Comet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl in: Comet_in_1: mzRecal2/mzRecal_out_1 Comet_in_2: input2 out: [Comet_out_1] PeptideProphet4: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: Comet3/Comet_out_1 # Manual edit: PeptideProphet_in_2: mzRecal3/mzRecal_out_1 @@ -42,7 +42,7 @@ steps: PeptideProphet_in_3: input2 out: [PeptideProphet_out_1] ProteinProphet5: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet4/PeptideProphet_out_1 # Manual edit: ProteinProphet_in_2: input2 diff --git a/examples/cwl-workflows/example8/workflow_8.cwl b/examples/cwl-workflows/example8/workflow_8.cwl index 058cc00..5cb2ba9 100644 --- a/examples/cwl-workflows/example8/workflow_8.cwl +++ b/examples/cwl-workflows/example8/workflow_8.cwl @@ -15,7 +15,7 @@ inputs: format: "http://edamontology.org/format_1929" # FASTA steps: MS_Amanda_01: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/MS_Amanda/MS_Amanda.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ms_amanda/ms_amanda.cwl in: MS_Amanda_in_1: input_1 MS_Amanda_in_2: input_2 @@ -26,14 +26,14 @@ steps: idconvert_in_1: MS_Amanda_01/MS_Amanda_out_1 out: [idconvert_out_1] PeptideProphet_03: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/PeptideProphet/PeptideProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/peptideprophet/peptideprophet.cwl in: PeptideProphet_in_1: idconvert_02/idconvert_out_1 PeptideProphet_in_2: input_1 PeptideProphet_in_3: input_2 out: [PeptideProphet_out_1, PeptideProphet_out_2] ProteinProphet_04: - run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ProteinProphet/ProteinProphet.cwl + run: https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/proteinprophet/proteinprophet.cwl in: ProteinProphet_in_1: PeptideProphet_03/PeptideProphet_out_1 ProteinProphet_in_2: input_2