Mercurial > repos > devteam > bamtools
changeset 2:ea3fc1adee75 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
---|---|
date | Wed, 11 Nov 2015 12:33:26 -0500 |
parents | c1a1bea37098 |
children | 04866f817daa |
files | bamtools.xml tool_dependencies.xml |
diffstat | 2 files changed, 46 insertions(+), 48 deletions(-) [+] |
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--- a/bamtools.xml Wed Aug 26 13:26:01 2015 -0400 +++ b/bamtools.xml Wed Nov 11 12:33:26 2015 -0500 @@ -1,19 +1,19 @@ <?xml version="1.0"?> -<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.1"> +<tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.2"> <description>BAM datasets and perform other transformations</description> <requirements> <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> - + <command> ##set up input files - + #for $bam_count, $input_bam in enumerate( $input_bams ): - ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" && - ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && + ln -s "${input_bam}" "localbam_${bam_count}.bam" && + ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && #end for - + #if str( $analysis_type.analysis_type_selector ) == "convert": #if str( $analysis_type.format_type.format_type_selector ) == "pileup": #set $reference_fasta_filename = "localref.fa" @@ -27,83 +27,81 @@ #end if ##finished setting up inputs - + ##start bamtools commandline - + bamtools - + #if str( $analysis_type.analysis_type_selector ) == "convert": - + convert - + -format ${analysis_type.format_type.format_type_selector} - + #if str( $analysis_type.format_type.format_type_selector ) == "pileup": - + ${analysis_type.format_type.mapqual} -fasta "${reference_fasta_filename}" - + #elif str( $analysis_type.format_type.format_type_selector ) == "sam": - + ${analysis_type.format_type.noheader} - + #end if - + -out $out_file1 - + #elif str( $analysis_type.analysis_type_selector ) == "count": - + count > $out_file1 - + #elif str( $analysis_type.analysis_type_selector ) == "coverage": - + coverage -out $out_file1 - + #elif str( $analysis_type.analysis_type_selector ) == "header": - + header > $out_file1 - + #elif str( $analysis_type.analysis_type_selector ) == "merge": - + merge -out $out_file1 - + #elif str( $analysis_type.analysis_type_selector ) == "random": - + random -n ${analysis_type.count} -seed ${analysis_type.seed} -out $out_file1 - + #elif str( $analysis_type.analysis_type_selector ) == "revert": - + revert ${analysis_type.keepDuplicate} ${analysis_type.keepQualities} -out $out_file1 - + #elif str( $analysis_type.analysis_type_selector ) == "sort": - + sort ${analysis_type.byname} -out $out_file1 - + #end if - + #for $bam_count, $input_bam in enumerate( $input_bams ): -in "localbam_${bam_count}.bam" #end for - - + + </command> <inputs> - - <repeat name="input_bams" title="BAM dataset(s) to filter" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM dataset" /> - </repeat> + + <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> <conditional name="analysis_type"> <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool"> @@ -179,7 +177,7 @@ <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/> </when> </conditional> - + </inputs> <outputs> <data format="txt" name="out_file1"> @@ -195,11 +193,11 @@ <when input="analysis_type.analysis_type_selector" value="revert" format="bam" /> <when input="analysis_type.analysis_type_selector" value="sort" format="bam" /> </change_format> - </data> + </data> </outputs> <tests> <test> - <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="convert"/> <param name="format_type_selector" value="pileup"/> <param name="reference_source_selector" value="history" /> @@ -208,26 +206,26 @@ <output name="output_bam" file="bamtools-convert-pileup.pu" /> </test> <test> - <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="count"/> <output name="output_bam" file="bamtools-count.tab" /> </test> <test> - <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="coverage"/> <output name="output_bam" file="bamtools-coverage.tab" /> </test> <test> - <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/> + <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="header"/> <output name="output_bam" file="bamtools-header.txt" /> </test> </tests> - + <stdio> <exit_code range="1:" /> </stdio> - + <help> **What is does**
--- a/tool_dependencies.xml Wed Aug 26 13:26:01 2015 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:33:26 2015 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="bamtools" version="2.3.0_2d7685d2ae"> - <repository changeset_revision="4e49af060657" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7d6da4982f19" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />