view countmatrixforedger.xml @ 0:c5a812cdf478 draft

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<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#

            cat script.data > /tmp/script.data;
            $__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="" help="" />
            <param name="sample_name" type="text" label="" help="" />
            <param name="sample_group" type="text" label="" help="" />
        </repeat>
    </inputs>
    <outputs>
<!--        <data name="output" format="data" /> -->
        <data name="count_matrix" format="data" />
        <data name="annotation" format="data" />
        <data name="log" format="data" />
        <data name="error_log" format="data" />
    </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="output" file="output"/>

        </test> -->
        <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[ 

tutaj cos bedzie
     ]]>
    </help>
        <citations>
        <citation type="bibtex">
            @article{Berenger2014,
              doi = {10.1186/1758-2946-6-23},
              url = {http://dx.doi.org/10.1186/1758-2946-6-23},
              year  = {2014},
              publisher = {Springer Nature},
              volume = {6},
              number = {1},
              pages = {23},
              author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
              title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
              journal = {Journal of Cheminformatics}
            }
        </citation>
    </citations>
</tool>