annotate biotradis_tradis_comparison.xml @ 10:4e8358bc80f9 draft

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 35e807998700f046b29e0b8100416cf6ea0f930b-dirty"

<tool id="tradis_comparison" name="tradis comparison" version="@VERSION@">
    <description>Compares two experimental conditions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    #for $counter, $input in enumerate($control):
            ln -s '$input' $input.element_identifier &&
            echo  ./$new_name >> control &&
    #end for
    
    #for $counter, $input in enumerate($conditions):
            ln -s '$input' $input.element_identifier &&
            echo  ./$new_name >> conditions &&
    #end for

    tradis_comparison.R 
    --controls control
    --conditions conditions
    -o output.csv
    -p plot.pdf
    #if str($filter.filter_selector)=="yes":
        -f
        -t $filter.cutoff
    #end if
    ]]>    </command>
    <inputs>
        <param name="control" type="data" format="csv" multiple="true" label="Control list"/>
        <param name="conditions" type="data" format="csv" multiple="true" label="Condition list"/>
        <conditional name="filter">
            <param name="filter_selector" type="select" label="Filter">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param name="cutoff" type="integer" min="0" value="0" label="Cut-off value"/>
            </when>
            <when value="no"/>
        </conditional>

    </inputs>

    <outputs>
        <data name="output" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="output.csv"/>
        <data name="plot" format="pdf" label="${tool.name} on ${on_string} Plot" from_work_dir="plot.pdf" />
    </outputs>

    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[
        Compares two experimental conditions using the method of Dembek et al.
        mBio 2015. Read counts per gene are compared using edgeR. This analysis
        requires experimental replicates.
    ]]>    </help>
    <expand macro="citations" />

</tool>