Mercurial > repos > iuc > stacks_pstacks
diff stacks_pstacks.xml @ 12:a9ff3d0184b8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author | iuc |
---|---|
date | Fri, 07 Apr 2023 22:01:24 +0000 |
parents | 67cbd80b83f5 |
children |
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--- a/stacks_pstacks.xml Tue Mar 22 23:21:58 2022 +0000 +++ b/stacks_pstacks.xml Fri Apr 07 22:01:24 2023 +0000 @@ -1,9 +1,9 @@ <tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0"> <description>find stacks from short reads mapped to a reference genome</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @@ -71,17 +71,11 @@ <inputs> <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" /> - <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/> - - <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/> - - <param name="max_clipped" argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/> - - <param name="min_mapq" argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/> - - <param name="keep_sec_alns" argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" /> - + <param argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/> + <param argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/> + <param argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/> + <param argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" /> <!-- SNP Model options --> <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False"> <expand macro="snp_options_full"/> @@ -90,9 +84,7 @@ <outputs> <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" /> - <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> - <collection name="tabs" type="list" label="Stacks from ${on_string}"> <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />