view hicup_deduplicator.xml @ 3:6551ad3d75f4 draft

planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit e6a9507eb198c6bf2c63ddae387c262bfc8dbd16

<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@.0">
    <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />
    <expand macro="stdio" />

    <command><![CDATA[
        hicup_deduplicator --quiet '$input_file'
        && mv *.dedup.* dataset.dedup_result
        && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt
        && mv *deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg
        && mv *deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="bam,sam" label="Input file(s)" help="Input files in bam or sam format."/>
    </inputs>
    <outputs>
       <data name="dedup_result" format="bam,sam" label="Deduplicator Result" from_work_dir="dataset.dedup_result" />
       <expand macro="deduplicator_output" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="dataset.filt.sam" ftype="sam"/>
            <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" />
            <output name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/>
            <output name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/>
            <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/>
        </test>
    </tests>
    <help><![CDATA[

    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/

    To get more information about the deduplicator visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Deduplicator
    ]]></help>
    <expand macro="citation_hicup" />
</tool>