Mercurial > repos > devteam > samtools_calmd
changeset 0:39472bc02d8d draft
Uploaded initial tool tarball.
| author | devteam |
|---|---|
| date | Wed, 24 Sep 2014 10:43:00 -0400 |
| parents | |
| children | c61c0d198e4a |
| files | samtools_calmd.xml test-data/phiX.bam test-data/phiX.fasta test-data/samtools_calmd_out_1.bam test-data/samtools_calmd_out_2.bam tool-data/fasta_indexes.loc.sample tool-data/tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 8 files changed, 246 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_calmd.xml Wed Sep 24 10:43:00 2014 -0400 @@ -0,0 +1,110 @@ +<tool id="samtools_calmd" name="Recalculate" version="1.0.0"> + <description>MD/NM tags and '=' bases</description> + <requirements> + <requirement type="package" version="1.0">samtools</requirement> + </requirements> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <command><![CDATA[ + #if str( $reference_source.reference_source_selector ) == "history": + #set ref_fa = 'ref.fa' + ln -s "${reference_source.ref_fasta}" ref.fa && samtools faidx ref.fa && + #else: + #set ref_fa = str( $reference_source.ref_fasta.fields.path ) + #end if + samtools calmd + #if str($option_set.option_sets) == 'advanced': + $option_set.change_identical $option_set.modify_quality $option_set.compute_cap $option_set.extended_baq + #end if + -b "$input_bam" "$ref_fa" > "$calmd_output" ]]> + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <inputs> + <param format="bam" name="input_bam" type="data" label="BAM file to recalculate" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference FASTA"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_fasta" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" column="value" key="dbkey" ref="input_bam" /> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> + </options> + </param> + </when> + <when value="history"> + <param name="ref_fasta" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <conditional name="option_set"> + <param name="option_sets" type="select" label="Options"> + <option value="default">Use defaults</option> + <option value="advanced">Advanced options</option> + </param> + <when value="default" /> + <when value="advanced"> + <param name="change_identical" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Change identical bases to '='" /> + <param name="modify_quality" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Modify the quality string" /> + <param name="compute_cap" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Compute BQ or cap baseQ by BAQ" /> + <param name="extended_baq" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ for better sensitivity" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="bam" name="calmd_output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="option_sets" value="default" /> + <param name="input_bam" value="phiX.bam" dbkey="phiX" /> + <param name="reference_source|reference_source_selector" value="history" /> + <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" /> + <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> + </test> + <!-- Using the test-data-repo's phiX.fa should produce the same output. --> + <test> + <param name="option_sets" value="default" /> + <param name="input_bam" value="phiX.bam" dbkey="phiX" /> + <param name="reference_source|reference_source_selector" value="cached" /> + <param name="ref_fasta" value="phiX" /> + <output name="calmd_output" file="samtools_calmd_out_1.bam" ftype="bam" /> + </test> + <test> + <param name="option_sets" value="advanced" /> + <param name="change_identical" value="true" /> + <param name="extended_baq" value="true" /> + <param name="input_bam" value="phiX.bam" dbkey="phiX" /> + <param name="reference_source|reference_source_selector" value="history" /> + <param name="ref_fasta" value="phiX.fasta" dbkey="phiX" /> + <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> + </test> + <!-- Using the test-data-repo's phiX.fa should, as before, produce the same output. --> + <test> + <param name="option_sets" value="advanced" /> + <param name="change_identical" value="true" /> + <param name="extended_baq" value="true" /> + <param name="input_bam" value="phiX.bam" dbkey="phiX" /> + <param name="reference_source|reference_source_selector" value="cached" /> + <param name="ref_fasta" value="phiX" /> + <output name="calmd_output" file="samtools_calmd_out_2.bam" ftype="bam" /> + </test> + </tests> + <help> +**What it does** + +Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Outputs a BAM file. + +------ + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + </help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Wed Sep 24 10:43:00 2014 -0400 @@ -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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Wed Sep 24 10:43:00 2014 -0400 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Wed Sep 24 10:43:00 2014 -0400 @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="utf-8"?> +<tables> + <table comment_char="#" name="fasta_indexes"> + <columns>value, dbkey, name, path</columns> + <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" /> + <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table> + +<table comment_char="#" name="fasta_indexes"> + <columns>value, dbkey, name, path</columns> + <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" /> + <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table> + +<table comment_char="#" name="fasta_indexes"> + <columns>value, dbkey, name, path</columns> + <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" /> + <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table> + +<table comment_char="#" name="fasta_indexes"> + <columns>value, dbkey, name, path</columns> + <file path="/afs/bx.psu.edu/user/d/dave/workspace/CleanGalaxy/tool-data/gaius.bx.psu.edu/repos/devteam/sam_to_bam/e400768b0a91/fasta_indexes.loc" /> + <tool_shed_repository><tool_shed>gaius.bx.psu.edu:9009</tool_shed><repository_name>sam_to_bam</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e400768b0a91</installed_changeset_revision></tool_shed_repository></table> +</tables> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 24 10:43:00 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.0"> + <repository changeset_revision="da217d52e81c" name="package_samtools_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>