annotate countmatrixforedger.xml @ 5:4cdaf6059e84 draft default tip

planemo upload

<tool id="countmatrixforedger" name="countMatrixForEdger" version="1.0">
    <description>Make a count matrix for edgeR</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        <![CDATA[ 
            #for $i, $s in enumerate( $sample )#
                echo -e ${s.sample_data}"\t"${s.sample_name}"\t"${s.sample_group} >> script.data;
            #end for#

            $__tool_directory__/tools/scrsh.sh script.data;

            cat count.matrix > $count_matrix;
            cat annotation > $annotation;
            cat script.log > $log;
            cat error.log > $error_log

        ]]>
    </command>
    <inputs>
        <repeat name="sample" title="">
            <param name="sample_data" type="data" format="data" label="Output matrix from EDGE-pro (out_rpkm)" />
            <param name="sample_name" type="text" label="" help="Sample name" />
            <param name="sample_group" type="text" label="" help="Sample group name- it has to be the same string for each sample of this group" />
        </repeat>
    </inputs>
    <outputs>
        <data name="count_matrix" format="tabular" label="countMatrixForEdger: count matrix"/>
        <data name="annotation" format="tabular" label="countMatrixForEdger: annotation"/>
        <data name="log" format="txt" label="countMatrixForEdger: log"/>
        <data name="error_log" format="txt" label="countMatrixForEdger: error log"/>
    </outputs>
    <tests>
        <test>
            <param name="sample_0|sample_data" value="data1" />
            <param name="sample_1|sample_data" value="data2" />
            <param name="sample_2|sample_data" value="data3" />
            <param name="sample_3|sample_data" value="data4" />
            <param name="sample_0|sample_name" value="sample1" />
            <param name="sample_1|sample_name" value="sample2" />
            <param name="sample_2|sample_name" value="sample3" />
            <param name="sample_3|sample_name" value="sample4" />            
            <param name="sample_0|sample_group" value="gr1" />
            <param name="sample_1|sample_group" value="gr1" />
            <param name="sample_2|sample_group" value="gr2" />
            <param name="sample_3|sample_group" value="gr2" />
            <output name="count_matrix" file="count.matrix"/>
            <output name="annotation" file="annotation"/>
            <output name="log" file="script.log"/>
            <output name="error_log" file="error.log"/>
        </test>

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

     ]]>
    </help>
        <citations>
        <citation>
        </citation>
    </citations>
</tool>