comparison hicBuildMatrix.xml @ 12:8bf84c4cb1cb draft

"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"

11:4ceaee0043a5

    <macros>
        <token name="@BINARY@">hicBuildMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" >
        <requirement type="package" version="1.6">samtools</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[

        mkdir ./QCfolder &&
        mkdir $qc.files_path &&

        &&
        mv $qc.files_path/hicQC.html $qc
        && mv $qc.files_path/*.log raw_qc
        && mv matrix.$outputFormat matrix
        #if $outBam_Boolean:
            && samtools sort ./unsorted.bam -o sorted.bam
        #end if

]]>
    </command>
    <inputs>

                <param name="binSize" value="5000"/>
            </conditional>
            <param name='outputFormat' value='h5'/>
            <param name='outBam_Boolean' value="True" />
            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
            <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
        </test>
    </tests>
    <help><![CDATA[

12:8bf84c4cb1cb

    <macros>
        <token name="@BINARY@">hicBuildMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" >
        <requirement type="package" version="1.9">samtools</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[

        mkdir ./QCfolder &&
        mkdir $qc.files_path &&

        &&
        mv $qc.files_path/hicQC.html $qc
        && mv $qc.files_path/*.log raw_qc
        && mv matrix.$outputFormat matrix
        #if $outBam_Boolean:
            && samtools sort -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
        #end if

]]>
    </command>
    <inputs>

                <param name="binSize" value="5000"/>
            </conditional>
            <param name='outputFormat' value='h5'/>
            <param name='outBam_Boolean' value="True" />
            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
            <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size" delta="50000"/>
            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
        </test>
    </tests>
    <help><![CDATA[