comparison libshuff.xml @ 1:a84c121a3b75 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

0:73a96aeacf46

    <description>Cramer-von Mises tests communities for the same structure</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        ## create symlinks to input datasets
        ln -s "$dist" dist.dat &&
        ln -s "$group" group.dat &&

        echo 'libshuff(

            #end if
            iters=$iters
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
    ]]></command>
    <inputs>
        <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
        <param name="groups" type="select" multiple="true" label="groups - Groups to condider">

<![CDATA[

@MOTHUR_OVERVIEW@


**Command Documenation**

The libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.

.. _libshuff: http://www.mothur.org/wiki/Libshuff

]]>
    </help>
    <expand macro="citations"/>
</tool>

1:a84c121a3b75

    <description>Cramer-von Mises tests communities for the same structure</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @SHELL_OPTIONS@

        ## create symlinks to input datasets
        ln -s "$dist" dist.dat &&
        ln -s "$group" group.dat &&

        echo 'libshuff(

            #end if
            iters=$iters
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
        <param name="groups" type="select" multiple="true" label="groups - Groups to condider">

<![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The libshuff_ method is a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic. The significance of the test statistic indicates the probability that the communities have the same structure by chance. Because each pairwise comparison requires two significance tests, a correction for multiple comparisons (e.g. Bonferroni's correction) must be applied.

.. _libshuff: https://www.mothur.org/wiki/Libshuff

]]>
    </help>
    <expand macro="citations"/>
</tool>