comparison structureharvester.xml @ 2:d926fce1459a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester commit f1cac0ad033da79288fe720fbe5af5948cc61d44

1:d6689391cd0c

<tool id="structureharvester" name="structureHarvester" version="0.6.94">
    <description>for parsing STRUCTURE outputs and for performing the Evanno method</description>
    <requirements>
        <requirement type="package" version="0.6.94">structureharvester</requirement>
    </requirements>
    <version_command><![CDATA[
        structureHarvester.py --version
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[

            ln -s '$input' 'inputs/$input.element_identifier' &&
        #end for
        structureHarvester.py --dir inputs/ --out . $evanno $clumpp &&
        mv summary.txt '$summary'
        #if $evanno
            && mv evanno.txt $evanno
        #end if
        #if $clumpp
            && mkdir clumpp_indfile clumpp_popfile
            && mv *.indfile clumpp_indfile/
            && mv *.popfile clumpp_popfile/

        <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" />
        <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."/>
        <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." />
    </inputs>
    <outputs>
        <data name="summary" format="txt" label="Structure Harvester summary"/>
        <data name="evanno" format="txt" label="Evann method output">
            <filter>evanno</filter>
        </data>
        <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile">
            <filter>clumpp</filter>
            <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" />
        </collection>
        <collection name="clumpp_popfile" type="list" label="Clumpp K*.popfile">
            <filter>clumpp</filter>
            <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" />
        </collection>
    </outputs>
    <tests>
        <test>
            <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" />
            <param name="evanno" value="false" />
            <param name="clumpp" value="true" />
            <output name="summary">
                <assert_contents>

    </tests>
    <help><![CDATA[

Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method.

.. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/
.. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html

    ]]></help>
    <citations>
        <citation type="doi">10.1007/s12686-011-9548-7</citation>

2:d926fce1459a

<tool id="structureharvester" name="structureHarvester" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>for parsing STRUCTURE outputs and for performing the Evanno method</description>
    <macros>
        <token name="@TOOL_VERSION@">0.6.94</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">structureharvester</requirement>
    </requirements>
    <version_command><![CDATA[
        structureHarvester.py --version
    ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[

            ln -s '$input' 'inputs/$input.element_identifier' &&
        #end for
        structureHarvester.py --dir inputs/ --out . $evanno $clumpp &&
        mv summary.txt '$summary'
        #if $evanno
            && mv evanno.txt '$evanno_out'
        #end if
        #if $clumpp
            && mkdir clumpp_indfile clumpp_popfile
            && mv *.indfile clumpp_indfile/
            && mv *.popfile clumpp_popfile/

        <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" />
        <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."/>
        <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." />
    </inputs>
    <outputs>
        <data name="summary" format="txt" label="${tool.name} on ${on_string}: Summary"/>
        <data name="evanno_out" format="txt" label="${tool.name} on ${on_string}: Evann output">
            <filter>evanno</filter>
        </data>
        <collection name="clumpp_indfile" type="list" label="${tool.name} on ${on_string}: Clumpp K*.indfile">
            <filter>clumpp</filter>
            <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" />
        </collection>
        <collection name="clumpp_popfile" type="list" label="${tool.name} on ${on_string}: Clumpp K*.popfile">
            <filter>clumpp</filter>
            <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" />
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <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" />
            <param name="evanno" value="false" />
            <param name="clumpp" value="true" />
            <output name="summary">
                <assert_contents>

    </tests>
    <help><![CDATA[

Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method.

.. _Structure_Harvester: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/
.. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html

    ]]></help>
    <citations>
        <citation type="doi">10.1007/s12686-011-9548-7</citation>