Mercurial > repos > devteam > bamtools_split
changeset 4:64ed37303c15 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools_split commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
| author | devteam |
|---|---|
| date | Wed, 18 Jan 2017 11:44:34 -0500 |
| parents | 10dcc8027778 |
| children | |
| files | bamtools-split.xml tool_dependencies.xml |
| diffstat | 2 files changed, 56 insertions(+), 74 deletions(-) [+] |
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--- a/bamtools-split.xml Mon Nov 09 12:04:47 2015 -0500 +++ b/bamtools-split.xml Wed Jan 18 11:44:34 2017 -0500 @@ -1,75 +1,63 @@ -<tool id="bamSplit" name="Split" version="0.0.2" force_history_refresh="True"> - <description>BAM datasets on variety of attributes</description> - <requirements> - <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> - </requirements> - <command> - - echo "BAM" > $report && - - #for $bam_count, $input_bam in enumerate( $input_bams ): - ln -s "${input_bam}" "localbam_${bam_count}.bam" && - ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && - #end for - - bamtools - split - - #if str ( $analysis_type.analysis_type_selector ) == "-tag" : - - ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" - - #else - - ${analysis_type.analysis_type_selector} - - #end if - - -stub split_bam - - #for $bam_count, $input_bam in enumerate( $input_bams ): - -in "localbam_${bam_count}.bam" - #end for - - </command> - - <inputs> - <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="Split BAM dataset(s) by" help="See help below for explanation of each option"> - <option value="-mapped">Mapping status (-mapped)</option> - <option value="-paired">Pairing status (-paired)</option> - <option value="-reference">Reference name (-reference)</option> - <option value="-tag">Specific tag (-tag)</option> - </param> - <when value="-mapped" /> - <when value="-paired" /> - <when value="-reference" /> - <when value="-tag"> - <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> - </when> - </conditional> - </inputs> - - <outputs> - <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> - <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> - </data> - </outputs> +<tool id="bamSplit" name="Split" version="2.4.0"> + <description>BAM datasets on variety of attributes</description> + <requirements> + <requirement type="package" version="2.4.0">bamtools</requirement> + </requirements> + <command> + <![CDATA[ + echo "BAM" > $report && + #for $bam_count, $input_bam in enumerate( $input_bams ): + ln -s "${input_bam}" "localbam_${bam_count}.bam" && + ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && + #end for + bamtools + split + #if str ( $analysis_type.analysis_type_selector ) == "-tag" : + ${analysis_type.analysis_type_selector} "${analysis_type.tag_name}" + #else + ${analysis_type.analysis_type_selector} + #end if + -stub split_bam + #for $bam_count, $input_bam in enumerate( $input_bams ): + -in "localbam_${bam_count}.bam" + #end for + ]]> + </command> + <inputs> + <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="Split BAM dataset(s) by" help="See help below for explanation of each option"> + <option value="-mapped">Mapping status (-mapped)</option> + <option value="-paired">Pairing status (-paired)</option> + <option value="-reference">Reference name (-reference)</option> + <option value="-tag">Specific tag (-tag)</option> + </param> + <when value="-mapped" /> + <when value="-paired" /> + <when value="-reference" /> + <when value="-tag"> + <param name="tag_name" type="text" value="NM" label="Enter tag name here" help="For example, to split on NM tag enter "NM""/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="report" label="BAMSplitter Run" hidden="true"> + <discover_datasets pattern="split_bam\.(?P<designation>.+)\.bam" ext="bam" visible="true"/> + </data> + </outputs> <tests> <test> <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> <param name="analysis_type_selector" value="-mapped"/> <output name="report"> - <assert_contents> - <has_line line="BAM" /> - </assert_contents> - <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> + <assert_contents> + <has_line line="BAM" /> + </assert_contents> + <discovered_dataset designation="MAPPED" file="bamtools-split-test1.bam" ftype="bam"/> </output> - </test> </tests> -<help> + <help> **What is does** BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). @@ -113,8 +101,8 @@ Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki -</help> - <citations> - <citation type="doi">10.1093/bioinformatics/btr174</citation> - </citations> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr174</citation> + </citations> </tool>
--- a/tool_dependencies.xml Mon Nov 09 12:04:47 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bamtools" version="2.3.0_2d7685d2ae"> - <repository changeset_revision="f1ce7a19eb68" name="package_bamtools_2_3_0_2d7685d2ae" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>