comparison libshuff.xml @ 2:ffe8649e5434 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

1:6050c5fade6a

    </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(
            phylip=dist.dat,
            group=group.dat,
            #if $groups:
                groups=${ str($groups).replace(",","-") },
            #end if
            sim=$sim,
            #if $form.form2 == "discrete":
                step=$form.step,
                #if $form.cutoff:
                    cutoff=$form.cutoff,
                #end if
            #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">

            <when value="discrete">
                <param name="step" type="float" value="0.10" min="0.0" max="1.0" label="step - Step size - ignored if not > 0" help="default value 0.10, smaller steps approach integral"/>
                <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary" format="tabular" from_work_dir="dist*.summary" label="${tool.name} on ${on_string}: summary"/>
        <data name="coverage" format="tabular" from_work_dir="dist*.coverage" label="${tool.name} on ${on_string}: coverage"/>

                    <has_text text="dist"/>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>

                    <has_text text="dist"/>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![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>

2:ffe8649e5434

    </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(
    phylip=dist.dat,
    group=group.dat,
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    sim=$sim,
    #if $form.form2 == "discrete":
        step=$form.step,
        #if $form.cutoff:
            cutoff=$form.cutoff,
        #end if
    #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">

            <when value="discrete">
                <param name="step" type="float" value="0.10" min="0.0" max="1.0" label="step - Step size - ignored if not > 0" help="default value 0.10, smaller steps approach integral"/>
                <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/>
            </when>
        </conditional>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary" format="tabular" from_work_dir="dist*.summary" label="${tool.name} on ${on_string}: summary"/>
        <data name="coverage" format="tabular" from_work_dir="dist*.coverage" label="${tool.name} on ${on_string}: coverage"/>

                    <has_text text="dist"/>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>

                    <has_text text="dist"/>
                    <has_text text="forest-pasture"/>
                    <has_text text="pasture-forest"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![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>