comparison filter_insertions.xml @ 42:5b8781514bc1 draft

planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 63220935ba51b0b5480da88017d58616bf671337-dirty

41:4fdf606153df

    </requirements>
    <version_command>confirm_insertions --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -fs $putative_insertions putative_insertions.gff &&
        ln -fs $all_insertions all_insertions.gff &&
        ln -fs $all_controls all_controls_path.gff &&
        confirm_insertions
        --putative_insertions_path putative_insertions.gff
        --all_treatments_path all_insertions.gff
        #for p in $all_controls
            --all_controls_paths '$p'
        #end for
        --output_path '$output'
        $output_discard
    ]]></command>
    <inputs>

42:5b8781514bc1

    </requirements>
    <version_command>confirm_insertions --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        ln -fs $putative_insertions putative_insertions.gff &&
        ln -fs $all_insertions all_insertions.gff &&
        #for i, p in enumerate($all_controls)
            ln -fs '$p' all_controls_${i}.gff &&
        #end for
        confirm_insertions
        --putative_insertions_path putative_insertions.gff
        --all_treatments_path all_insertions.gff
        #for i, p in enumerate($all_controls)
            --all_controls_paths all_controls_${i}.gff
        #end for
        --output_path '$output'
        $output_discard
    ]]></command>
    <inputs>