Mercurial > repos > iuc > stacks_pstacks

comparison stacks_pstacks.xml @ 9:ed2fba238a2f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 21:54:20 +0000
parents 7519668b19d7
children
comparison
equal deleted inserted replaced
8:7519668b19d7 9:ed2fba238a2f
1 <tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0">
2 <description>find stacks from short reads mapped to a reference genome</description> 2 <description>find stacks from short reads mapped to a reference genome</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 10
11 @CLEAN_EXT@ 11 @CLEAN_EXT@
69 stacks_summary.py --stacks-prog pstacks --res-dir stacks_outputs --logfile pstacks.log --summary stacks_outputs/summary.html 69 stacks_summary.py --stacks-prog pstacks --res-dir stacks_outputs --logfile pstacks.log --summary stacks_outputs/summary.html
70 ]]></command> 70 ]]></command>
71 71
72 <inputs> 72 <inputs>
73 <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" /> 73 <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" />
74
75 <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/> 74 <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
76 75 <param argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/>
77 <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/> 76 <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"/>
78 77 <param argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>
79 <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"/> 78 <param argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />
80
81 <param name="min_mapq" argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>
82
83 <param name="keep_sec_alns" argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />
84
85 <!-- SNP Model options --> 79 <!-- SNP Model options -->
86 <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False"> 80 <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False">
87 <expand macro="snp_options_full"/> 81 <expand macro="snp_options_full"/>
88 </section> 82 </section>
89 </inputs> 83 </inputs>
90 84
91 <outputs> 85 <outputs>
92 <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" /> 86 <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
93
94 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> 87 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
95
96 <collection name="tabs" type="list" label="Stacks from ${on_string}"> 88 <collection name="tabs" type="list" label="Stacks from ${on_string}">
97 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> 89 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
98 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> 90 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
99 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> 91 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
100 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" /> 92 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />