-
Notifications
You must be signed in to change notification settings - Fork 441
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'galaxyproject:main' into seqtk_mergefa_toolshed_edit
- Loading branch information
Showing
182 changed files
with
14,845 additions
and
4,560 deletions.
There are no files selected for viewing
14 changes: 14 additions & 0 deletions
14
data_managers/data_manager_bwa_mem2_index_builder/.shed.yml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| categories: | ||
| - Data Managers | ||
| description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. | ||
| homepage_url: https://github.com/bwa-mem2/bwa-mem2 | ||
| long_description: | | ||
| Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces | ||
| alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, | ||
| dataset and the running machine. Bwa-mem2 uses a different index format that | ||
| is efficient on disk space and runtime memory but requires larger amounts of | ||
| memory (roughly 27x the reference) when building. | ||
| name: data_manager_bwa_mem2_index_builder | ||
| owner: iuc | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder | ||
| type: unrestricted |
75 changes: 75 additions & 0 deletions
75
data_managers/data_manager_bwa_mem2_index_builder/data_manager/bwa_mem2_index_builder.xml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| <tool id="bwa_mem2_index_builder_data_manager" name="Build BWA-MEM2 indexes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05"> | ||
| <description></description> | ||
| <macros> | ||
| <token name="@TOOL_VERSION@">2.2.1</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| </macros> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement> | ||
| </requirements> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] | ||
| mkdir -p '${out_file.extra_files_path}' && | ||
| ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && | ||
| bwa-mem2 index '${out_file.extra_files_path}/${fasta_file_name}' && | ||
| cp '$dmjson' '$out_file' | ||
| ]]> | ||
| </command> | ||
| <configfiles> | ||
| <configfile name="dmjson"><![CDATA[#slurp | ||
| #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1] | ||
| #set $value = $sequence_id or $all_fasta_source.fields.dbkey | ||
| #set $name = $sequence_name or $all_fasta_source.fields.name | ||
| { | ||
| "data_tables":{ | ||
| "bwa_mem2_indexes":[ | ||
| { | ||
| "value": "${value}", | ||
| "dbkey": "${all_fasta_source.fields.dbkey}", | ||
| "name": "${name}", | ||
| "path": "${fasta_file_name}" | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| ]]></configfile> | ||
| </configfiles> | ||
| <inputs> | ||
| <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | ||
| <options from_data_table="all_fasta"/> | ||
| </param> | ||
| <param name="sequence_name" type="text" value="" label="Name of sequence" /> | ||
| <param name="sequence_id" type="text" value="" label="ID for sequence" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="out_file" format="data_manager_json" /> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="all_fasta_source" value="phiX174"/> | ||
| <output name="out_file" file="bwa_mem2_data_manager.1.json"/> | ||
| </test> | ||
| <test> | ||
| <param name="all_fasta_source" value="phiX174"/> | ||
| <param name="sequence_name" value="Galeocerdo cuvier"/> | ||
| <param name="sequence_id" value="fooBar1"/> | ||
| <output name="out_file" file="bwa_mem2_data_manager.2.json"/> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| <![CDATA[ | ||
| .. class:: infomark | ||
| **Notice:** If you leave name, description, or id blank, it will be generated automatically. | ||
| Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces | ||
| alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, | ||
| dataset and the running machine. Bwa-mem2 uses a different index format that | ||
| is efficient on disk space and runtime memory but requires larger amounts of | ||
| memory (roughly 27x the reference) when building. | ||
| ]]> | ||
| </help> | ||
| <citations> | ||
| <citation type="doi">10.1038/nmeth.3317</citation> | ||
| </citations> | ||
| </tool> |
20 changes: 20 additions & 0 deletions
20
data_managers/data_manager_bwa_mem2_index_builder/data_manager_conf.xml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| <?xml version="1.0"?> | ||
| <data_managers> | ||
| <data_manager tool_file="data_manager/bwa_mem2_index_builder.xml" id="bwa_mem2_index_builder"> | ||
| <data_table name="bwa_mem2_indexes"> | ||
| <output> | ||
| <column name="value" /> | ||
| <column name="dbkey" /> | ||
| <column name="name" /> | ||
| <column name="path" output_ref="out_file" > | ||
| <move type="directory" relativize_symlinks="True"> | ||
| <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> | ||
| <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/bwa_mem2_index/${value}</target> | ||
| </move> | ||
| <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bwa_mem2_index/${value}/${path}</value_translation> | ||
| <value_translation type="function">abspath</value_translation> | ||
| </column> | ||
| </output> | ||
| </data_table> | ||
| </data_manager> | ||
| </data_managers> |
19 changes: 19 additions & 0 deletions
19
data_managers/data_manager_bwa_mem2_index_builder/test-data/all_fasta.loc
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| #This file lists the locations and dbkeys of all the fasta files | ||
| #under the "genome" directory (a directory that contains a directory | ||
| #for each build). The script extract_fasta.py will generate the file | ||
| #all_fasta.loc. This file has the format (white space characters are | ||
| #TAB characters): | ||
| # | ||
| #<unique_build_id> <dbkey> <display_name> <file_path> | ||
| # | ||
| #So, all_fasta.loc could look something like this: | ||
| # | ||
| #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa | ||
| #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa | ||
| #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa | ||
| # | ||
| #Your all_fasta.loc file should contain an entry for each individual | ||
| #fasta file. So there will be multiple fasta files for each build, | ||
| #such as with hg19 above. | ||
| # | ||
| phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta |
12 changes: 12 additions & 0 deletions
12
data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.1.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| { | ||
| "data_tables":{ | ||
| "bwa_mem2_indexes":[ | ||
| { | ||
| "value": "phiX174", | ||
| "dbkey": "phiX174", | ||
| "name": "phiX174", | ||
| "path": "phiX174.fasta" | ||
| } | ||
| ] | ||
| } | ||
| } |
12 changes: 12 additions & 0 deletions
12
data_managers/data_manager_bwa_mem2_index_builder/test-data/bwa_mem2_data_manager.2.json
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| { | ||
| "data_tables":{ | ||
| "bwa_mem2_indexes":[ | ||
| { | ||
| "value": "fooBar1", | ||
| "dbkey": "phiX174", | ||
| "name": "Galeocerdo cuvier", | ||
| "path": "phiX174.fasta" | ||
| } | ||
| ] | ||
| } | ||
| } |
Empty file.
79 changes: 79 additions & 0 deletions
79
data_managers/data_manager_bwa_mem2_index_builder/test-data/phiX174.fasta
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| >phiX174 | ||
| GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT | ||
| GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA | ||
| ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG | ||
| TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA | ||
| GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC | ||
| TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT | ||
| TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT | ||
| CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT | ||
| TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG | ||
| TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC | ||
| GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA | ||
| CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG | ||
| TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT | ||
| AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC | ||
| CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA | ||
| TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC | ||
| TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA | ||
| CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA | ||
| GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT | ||
| GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA | ||
| ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC | ||
| TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT | ||
| TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC | ||
| ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC | ||
| CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT | ||
| GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC | ||
| CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC | ||
| TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG | ||
| TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT | ||
| TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA | ||
| AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT | ||
| TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT | ||
| ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC | ||
| GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC | ||
| TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT | ||
| TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA | ||
| TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG | ||
| TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC | ||
| CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG | ||
| AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC | ||
| CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT | ||
| TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG | ||
| CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA | ||
| AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT | ||
| GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG | ||
| GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA | ||
| TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT | ||
| CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG | ||
| TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA | ||
| GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC | ||
| CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA | ||
| TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA | ||
| AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC | ||
| TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT | ||
| CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA | ||
| TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG | ||
| TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT | ||
| CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT | ||
| TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC | ||
| ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG | ||
| TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA | ||
| ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG | ||
| GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC | ||
| CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT | ||
| GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG | ||
| GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT | ||
| ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG | ||
| CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC | ||
| CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC | ||
| GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT | ||
| CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG | ||
| CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA | ||
| TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT | ||
| TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG | ||
| TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC | ||
| AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC | ||
| TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA | ||
|
|
18 changes: 18 additions & 0 deletions
18
data_managers/data_manager_bwa_mem2_index_builder/tool-data/all_fasta.loc.sample
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| #This file lists the locations and dbkeys of all the fasta files | ||
| #under the "genome" directory (a directory that contains a directory | ||
| #for each build). The script extract_fasta.py will generate the file | ||
| #all_fasta.loc. This file has the format (white space characters are | ||
| #TAB characters): | ||
| # | ||
| #<unique_build_id> <dbkey> <display_name> <file_path> | ||
| # | ||
| #So, all_fasta.loc could look something like this: | ||
| # | ||
| #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa | ||
| #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa | ||
| #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa | ||
| # | ||
| #Your all_fasta.loc file should contain an entry for each individual | ||
| #fasta file. So there will be multiple fasta files for each build, | ||
| #such as with hg19 above. | ||
| # |
38 changes: 38 additions & 0 deletions
38
data_managers/data_manager_bwa_mem2_index_builder/tool-data/bwa_mem2_index.loc.sample
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| #This is a sample file distributed with Galaxy that enables tools | ||
| #to use a directory of BWA indexed sequences data files. You will need | ||
| #to create these data files and then create a bwa_index.loc file | ||
| #similar to this one (store it in this directory) that points to | ||
| #the directories in which those files are stored. The bwa_index.loc | ||
| #file has this format (longer white space characters are TAB characters): | ||
| # | ||
| #<unique_build_id> <dbkey> <display_name> <file_path> | ||
| # | ||
| #So, for example, if you had phiX indexed stored in | ||
| #/depot/data2/galaxy/phiX/base/, | ||
| #then the bwa_index.loc entry would look like this: | ||
| # | ||
| #phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa | ||
| # | ||
| #and your /depot/data2/galaxy/phiX/base/ directory | ||
| #would contain phiX.fa.* files: | ||
| # | ||
| #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb | ||
| #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann | ||
| #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt | ||
| #...etc... | ||
| # | ||
| #Your bwa_index.loc file should include an entry per line for each | ||
| #index set you have stored. The "file" in the path does not actually | ||
| #exist, but it is the prefix for the actual index files. For example: | ||
| # | ||
| #phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa | ||
| #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa | ||
| #hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa | ||
| #/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa | ||
| #...etc... | ||
| # | ||
| #Note that for backwards compatibility with workflows, the unique ID of | ||
| #an entry must be the path that was in the original loc file, because that | ||
| #is the value stored in the workflow for that parameter. That is why the | ||
| #hg19 entry above looks odd. New genomes can be better-looking. | ||
| # |
8 changes: 8 additions & 0 deletions
8
data_managers/data_manager_bwa_mem2_index_builder/tool_data_table_conf.xml.sample
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> | ||
| <tables> | ||
| <!-- Locations of indexes in the BWA-MEM2 mapper format--> | ||
| <table name="bwa_mem2_indexes" comment_char="#"> | ||
| <columns>value, dbkey, name, path</columns> | ||
| <file path="tool-data/bwa_mem2_index.loc" /> | ||
| </table> | ||
| </tables> |
12 changes: 12 additions & 0 deletions
12
data_managers/data_manager_bwa_mem2_index_builder/tool_data_table_conf.xml.test
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| <tables> | ||
| <!-- Locations of all fasta files under genome directory --> | ||
| <table name="all_fasta" comment_char="#"> | ||
| <columns>value, dbkey, name, path</columns> | ||
| <file path="${__HERE__}/test-data/all_fasta.loc" /> | ||
| </table> | ||
| <!-- Locations of indexes in the BWA-MEM2 mapper format--> | ||
| <table name="bwa_mem2_indexes" comment_char="#"> | ||
| <columns>value, dbkey, name, path</columns> | ||
| <file path="${__HERE__}/test-data/bwa_mem2_index.loc" /> | ||
| </table> | ||
| </tables> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.