preEBseq/EBA_wrapper_preEBSeq.xml at master · rlegendre/preEBseq · GitHub

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<tool id="preEBSeq" name="Preprocess files for EBSeq" version="0.1.0">
    <description>Generate expression matrix and IGvector file for EBSeq</description>
    <command interpreter="python">
        pre_EBSeq.py
        --outtable=$outtable
        --outvector=$outvector
            #for $j, $input_rep in enumerate ( $rep_counts ):
                --inputs  "${input_rep.count_data}" "${input_rep.label}"
            #end for

    </command>
    <inputs>
        <repeat name="rep_counts" title="Raw counts" min="2">
            <param name="count_data" type="data" format="txt" label="Raw count"/>
            <param name="label" format="txt" type="text" value="file1" label="File label name" help="You need to specify an unique label name for your replicates.">
                <sanitizer>
                    <valid initial="string.letters,string.digits">
                        <add value="_" />
                    </valid>
                    <mapping initial="none">
                        <add source=" " target="_"/>
                    </mapping>
                </sanitizer>
            </param>
        </repeat>

    </inputs>

    <outputs>
        <data format="tabular" name="outtable" label="Expression matrix (on ${on_string})" />
        <data format="tabular" name="outvector" label="IGvector file (on ${on_string})"/>
    </outputs>
    <tests>
        <test>

        </test>
    </tests>
    <help>
-----------
Description
-----------
Build Expression Table and IGvector fles from RSEM output to EBSeq input

    </help>
</tool>