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comparison structure.xml @ 3:4bd5e5dbc6c5 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure commit f03b7df7b3e4fd099ae0e1bd195c41ab2e0fa227"
author iuc
date Sun, 20 Mar 2022 10:57:34 +0000
parents 0080ad37f8a0
children
comparison
equal deleted inserted replaced
2:0080ad37f8a0 3:4bd5e5dbc6c5
1 <tool id="structure" name="Structure" version="2.3.4"> 1 <tool id="structure" name="Structure" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>using multi-locus genotype data to investigate population structure</description> 2 <description>using multi-locus genotype data to investigate population structure</description>
3 <xrefs>
4 <xref type="bio.tools">structure</xref>
5 </xrefs>
6 <macros>
7 <token name="@TOOL_VERSION@">2.3.4</token>
8 <token name="@VERSION_SUFFIX@">1</token>
9 </macros>
3 <requirements> 10 <requirements>
4 <requirement type="package" version="2.3.4">structure</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">structure</requirement>
5 </requirements> 12 </requirements>
6 <version_command><![CDATA[ 13 <version_command><![CDATA[
7 structure | grep -E -o 'Version.+' 14 structure | grep -E -o 'Version.+'
8 ]]></version_command> 15 ]]></version_command>
9 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
10 mv '$mainparams' '$out_mainparams' && 17 cp '$mainparams' '$out_mainparams' &&
11 mv '$extraparams' '$out_extraparams' && 18 cp '$extraparams' '$out_extraparams' &&
12 19
13 mkdir out log 20 mkdir out log
14 21
15 #for $run in range(1, int($nb_run) + 1): 22 #for $run in range(1, int($nb_run) + 1):
16 && structure -i '$infile' -o outfile -m '$out_mainparams' -e '$out_extraparams' > 'log/K_${main.MAXPOPS}_run_${run}_f.log' 23 && structure -i '$infile' -o outfile -m '$out_mainparams' -e '$out_extraparams' > 'log/K_${main.MAXPOPS}_run_${run}_f.log'
218 #define REPORTHITRATE $extra.REPORTHITRATE // default:0 // (B) report hit rate if using METROFREQ 225 #define REPORTHITRATE $extra.REPORTHITRATE // default:0 // (B) report hit rate if using METROFREQ
219 226
220 ]]></configfile> 227 ]]></configfile>
221 </configfiles> 228 </configfiles>
222 <inputs> 229 <inputs>
223 <param name="infile" type="data" label="Genotype data" format="tabular" /> 230 <param name="infile" type="data" label="Genotype data" format="txt,tabular" />
224 <param name="nb_run" value="1" type="integer" label="Number of runs" min="1" max="10" help="Note that the runs are sequential. Please launch separate runs if it's too long" /> 231 <param name="nb_run" value="1" type="integer" label="Number of runs" min="1" max="10" help="Note that the runs are sequential. Please launch separate runs if it's too long" />
225 <section name="main" title="mainparams" expanded="True"> 232 <section name="main" title="mainparams" expanded="True">
226 <!--Basic Program Parameters--> 233 <!--Basic Program Parameters-->
227 <param argument="MAXPOPS" value="" type="integer" label="Number of populations assumed" help="or [K]"/> 234 <param argument="MAXPOPS" value="" type="integer" label="Number of populations assumed" help="or [K]"/>
228 <param argument="BURNIN" value="10000" type="integer" label="Length of burnin period" /> 235 <param argument="BURNIN" value="10000" type="integer" label="Length of burnin period" />