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Add bio.tools for peptideshaker #749

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Add bio.tools for peptideshaker #749

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e38da08
Add bio.tools for peptideshaker
bebatut Mar 11, 2024
75d946a
Merge branch 'master' into peptideshaker
bgruening Mar 12, 2024
d3f862c
Merge branch 'master' into peptideshaker
bebatut Mar 18, 2024
06c0714
Try to fix linting
bebatut Mar 18, 2024
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7 changes: 5 additions & 2 deletions tools/peptideshaker/fasta_cli.xml
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Expand Up @@ -9,8 +9,9 @@
<macros>
<import>macros_basic.xml</import>
</macros>
<expand macro="xrefs"/>
<requirements>
<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
</requirements>
<expand macro="stdio" />
<command>
Expand Down Expand Up @@ -66,7 +67,9 @@
<tests>
<test>
<param name="input_database" value="fastacli_searchgui_tinydb1.fasta" ftype="fasta"/>
<output name="input_database_concatenated_target_decoy" file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
<output name="input_database_concatenated_target_decoy">
<discovered_dataset file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000"/>
</output>
</test>
</tests>
<help>
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3 changes: 2 additions & 1 deletion tools/peptideshaker/ident_params.xml
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Expand Up @@ -10,6 +10,7 @@
<import>macros_basic.xml</import>
<import>macros_modifications.xml</import>
</macros>
<expand macro="xrefs"/>
<requirements>
<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
</requirements>
Expand Down Expand Up @@ -653,7 +654,7 @@
<option value="Trypsin">Trypsin</option>
<option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
<option value="Arg-C">Arg-C</option>
<option value="Arg-C (no P rule)">Arg-C</option>
<option value="Arg-C (no P rule)">Arg-C (no P rule)</option>
<option value="Arg-N">Arg-N</option>
<option value="Glu-C">Glu-C</option>
<option value="Lys-C">Lys-C</option>
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5 changes: 5 additions & 0 deletions tools/peptideshaker/macros_basic.xml
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Expand Up @@ -15,6 +15,11 @@
<token name="@SEARCHGUI_VERSION_SUFFIX@">1</token>
<token name="@PEPTIDESHAKER_VERSION@">2.0.33</token>
<token name="@PEPTIDESHAKER_VERSION_SUFFIX@">1</token>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">peptideshaker</xref>
</xrefs>
</xml>
<xml name="citations">
<citations>
<citation type="doi">10.1186/1471-2105-12-70</citation>
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3 changes: 1 addition & 2 deletions tools/peptideshaker/macros_modifications.xml
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Expand Up @@ -119,15 +119,14 @@
<option value="Sulfation of T">Sulfation of T</option>
<option value="Sulfation of Y">Sulfation of Y</option>
<option value="S-nitrosylation">S-nitrosylation</option>
<option value="TMT 10-plex of K">TMT 10-plex of K</option>
<option value="TMT 10-plex of peptide N-term">TMT 10-plex of peptide N-term</option>
<option value="TMT 2-plex of K">TMT 2-plex of K</option>
<option value="TMT 2-plex of peptide N-term">TMT 2-plex of peptide N-term</option>
<option value="TMT 6-plex of K">TMT 6-plex of K</option>
<option value="TMT 6-plex of K+4">TMT 6-plex of K+4</option>
<option value="TMT 6-plex of K+6">TMT 6-plex of K+6</option>
<option value="TMT 6-plex of K+8">TMT 6-plex of K+8</option>
<option value="TMT 6-plex of peptide N-term">TMT 6-plex of peptide N-term</option>
<option value="TMT 10-plex of K">TMT 10-plex of K</option>
<option value="TMT 10-plex of K+4">TMT 10-plex of K+4</option>
<option value="TMT 10-plex of K+6">TMT 10-plex of K+6</option>
<option value="TMT 10-plex of K+8">TMT 10-plex of K+8</option>
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11 changes: 9 additions & 2 deletions tools/peptideshaker/peptide_shaker.xml
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Expand Up @@ -11,6 +11,7 @@
<import>macros_basic.xml</import>
<import>macros_modifications.xml</import>
</macros>
<expand macro="xrefs"/>
<requirements>
<requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
<requirement type="package">unzip</requirement>
Expand Down Expand Up @@ -294,7 +295,10 @@
<section name="exporting_options" expanded="true" title="Exporting options" help="All different outputs PeptideShaker may produce">

<conditional name="zip_conditional">
<param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
<param name="zip_output_boolean" type="select" label="Compress results into a single zip file">
<option value="zip">Yes</option>
<option value="separate" selected="true">No</option>
</param>
<when value="separate">
<param name="export_psdb" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports PeptideShakers‘ .psdb file" />
</when>
Expand All @@ -305,7 +309,10 @@
</conditional>

<conditional name="mzidentml_conditional">
<param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
<param name="mzidentml_creation" type="select" label="Creates a mzIdentML file">
<option value="1">Yes</option>
<option value="0">No</option>
</param>
<when value="1">
<param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />

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1 change: 1 addition & 0 deletions tools/peptideshaker/searchgui.xml
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Expand Up @@ -9,6 +9,7 @@
<macros>
<import>macros_basic.xml</import>
</macros>
<expand macro="xrefs"/>
<requirements>
<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
<requirement type="package" version="3.0">zip</requirement>
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