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comparison structureharvester.xml @ 2:28b9809c4002 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit f1cac0ad033da79288fe720fbe5af5948cc61d44
author iuc
date Wed, 25 Sep 2024 15:36:50 +0000
parents 8dc371b783eb
children
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1:8dc371b783eb 2:28b9809c4002
1 <tool id="structureharvester" name="structureHarvester" version="0.6.94"> 1 <tool id="structureharvester" name="structureHarvester" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>for parsing STRUCTURE outputs and for performing the Evanno method</description> 2 <description>for parsing STRUCTURE outputs and for performing the Evanno method</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.6.94</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="0.6.94">structureharvester</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">structureharvester</requirement>
5 </requirements> 9 </requirements>
6 <version_command><![CDATA[ 10 <version_command><![CDATA[
7 structureHarvester.py --version 11 structureHarvester.py --version
8 ]]></version_command> 12 ]]></version_command>
9 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$input' 'inputs/$input.element_identifier' && 16 ln -s '$input' 'inputs/$input.element_identifier' &&
13 #end for 17 #end for
14 structureHarvester.py --dir inputs/ --out . $evanno $clumpp && 18 structureHarvester.py --dir inputs/ --out . $evanno $clumpp &&
15 mv summary.txt '$summary' 19 mv summary.txt '$summary'
16 #if $evanno 20 #if $evanno
17 && mv evanno.txt $evanno 21 && mv evanno.txt '$evanno_out'
18 #end if 22 #end if
19 #if $clumpp 23 #if $clumpp
20 && mkdir clumpp_indfile clumpp_popfile 24 && mkdir clumpp_indfile clumpp_popfile
21 && mv *.indfile clumpp_indfile/ 25 && mv *.indfile clumpp_indfile/
22 && mv *.popfile clumpp_popfile/ 26 && mv *.popfile clumpp_popfile/
26 <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" /> 30 <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" />
27 <param argument="--evanno" type="boolean" checked="false" truevalue="--evanno" falsevalue="" label="If possible, performs the Evanno 2005 method." help="You must test at least 3 values of K. K values must be sequential. The number of replicates per K > 1."/> 31 <param argument="--evanno" type="boolean" checked="false" truevalue="--evanno" falsevalue="" label="If possible, performs the Evanno 2005 method." help="You must test at least 3 values of K. K values must be sequential. The number of replicates per K > 1."/>
28 <param argument="--clumpp" type="boolean" checked="false" truevalue="--clumpp" falsevalue="" label="Generates one K*.indfile for each value of K run, for use with CLUMPP." /> 32 <param argument="--clumpp" type="boolean" checked="false" truevalue="--clumpp" falsevalue="" label="Generates one K*.indfile for each value of K run, for use with CLUMPP." />
29 </inputs> 33 </inputs>
30 <outputs> 34 <outputs>
31 <data name="summary" format="txt" label="Structure Harvester summary"/> 35 <data name="summary" format="txt" label="${tool.name} on ${on_string}: Summary"/>
32 <data name="evanno" format="txt" label="Evann method output"> 36 <data name="evanno_out" format="txt" label="${tool.name} on ${on_string}: Evann output">
33 <filter>evanno</filter> 37 <filter>evanno</filter>
34 </data> 38 </data>
35 <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile"> 39 <collection name="clumpp_indfile" type="list" label="${tool.name} on ${on_string}: Clumpp K*.indfile">
36 <filter>clumpp</filter> 40 <filter>clumpp</filter>
37 <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" /> 41 <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" />
38 </collection> 42 </collection>
39 <collection name="clumpp_popfile" type="list" label="Clumpp K*.popfile"> 43 <collection name="clumpp_popfile" type="list" label="${tool.name} on ${on_string}: Clumpp K*.popfile">
40 <filter>clumpp</filter> 44 <filter>clumpp</filter>
41 <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" /> 45 <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" />
42 </collection> 46 </collection>
43 </outputs> 47 </outputs>
44 <tests> 48 <tests>
45 <test> 49 <test expect_num_outputs="3">
46 <param name="inputs" value="example_harvester_archive/Admix_run_001_f,example_harvester_archive/Admix_run_002_f,example_harvester_archive/Admix_run_004_f,example_harvester_archive/Admix_run_005_f,example_harvester_archive/Admix_run_007_f,example_harvester_archive/Admix_run_008_f,example_harvester_archive/K1ReRun_run_1_f,example_harvester_archive/K1ReRun_run_2_f" /> 50 <param name="inputs" value="example_harvester_archive/Admix_run_001_f,example_harvester_archive/Admix_run_002_f,example_harvester_archive/Admix_run_004_f,example_harvester_archive/Admix_run_005_f,example_harvester_archive/Admix_run_007_f,example_harvester_archive/Admix_run_008_f,example_harvester_archive/K1ReRun_run_1_f,example_harvester_archive/K1ReRun_run_2_f" />
47 <param name="evanno" value="false" /> 51 <param name="evanno" value="false" />
48 <param name="clumpp" value="true" /> 52 <param name="clumpp" value="true" />
49 <output name="summary"> 53 <output name="summary">
50 <assert_contents> 54 <assert_contents>
87 </tests> 91 </tests>
88 <help><![CDATA[ 92 <help><![CDATA[
89 93
90 Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method. 94 Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method.
91 95
92 .. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/ 96 .. _Structure_Harvester: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/
93 .. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html 97 .. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html
94 98
95 ]]></help> 99 ]]></help>
96 <citations> 100 <citations>
97 <citation type="doi">10.1007/s12686-011-9548-7</citation> 101 <citation type="doi">10.1007/s12686-011-9548-7</citation>