Mercurial > repos > iuc > stacks_refmap

comparison stacks_refmap.xml @ 9:f134c45859a8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 21:55:26 +0000
parents 0d516bfea0f2
children
comparison
equal deleted inserted replaced
8:0d516bfea0f2 9:f134c45859a8
1 <tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">
2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</description> 2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</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@
149 <param name="individual_sample" format="sam,bam" type="data" multiple="true" label="Files containing an individual sample from a population" argument="-s" help="Dataset names will be used as sample name (no space allowed)." /> 149 <param name="individual_sample" format="sam,bam" type="data" multiple="true" label="Files containing an individual sample from a population" argument="-s" help="Dataset names will be used as sample name (no space allowed)." />
150 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-O" /> 150 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-O" />
151 </when> 151 </when>
152 </conditional> 152 </conditional>
153 153
154 <param name="m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" argument="-m" /> 154 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" />
155 <param name="P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" argument="-P" /> 155 <param argument="-P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" />
156 156
157 <!-- SNP Model options --> 157 <!-- SNP Model options -->
158 <section name="snp_options" title="SNP_Model_Options" expanded="False"> 158 <section name="snp_options" title="SNP_Model_Options" expanded="False">
159 <expand macro="snp_options"/> 159 <expand macro="snp_options"/>
160 </section> 160 </section>