Mercurial > repos > devteam > picard
diff picard_DownsampleSam.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_DownsampleSam.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_DownsampleSam.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,47 +1,42 @@ -<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>Downsample a file to retain a subset of the reads</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ +<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>Downsample a file to retain a subset of the reads</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ picard DownsampleSam - INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" - PROBABILITY=${probability} - RANDOM_SEED=${seed} - QUIET=true - VERBOSITY=ERROR - VALIDATION_STRINGENCY=${validation_stringency} + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --PROBABILITY ${probability} + --RANDOM_SEED ${seed} + --QUIET true + --VERBOSITY ERROR + --VALIDATION_STRINGENCY ${validation_stringency} ]]></command> - <inputs> - <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" /> - <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" /> - <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" /> - - <expand macro="VS" /> - - </inputs> - - - <outputs> - <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/> - </outputs> - - <tests> - <test> - <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" /> - <param name="probability" value="0.1" /> - <param name="seed" value="1024" /> - <param name="validation_stringency" value="LENIENT" /> - <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/> - </test> - </tests> - <help> + <inputs> + <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset"/> + <param name="probability" type="float" min="0.0" max="1.0" value="1" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads"/> + <param name="seed" type="integer" value="1" label="Random seed value" help="RANDOM_SEED; default=1"/> + <expand macro="VS"/> + </inputs> + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/> + </outputs> + <tests> + <test> + <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam"/> + <param name="probability" value="0.1"/> + <param name="seed" value="1024"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + <help> .. class:: infomark @@ -70,5 +65,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>