view hicBuildMatrix.xml @ 0:611b0f02e109 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty

<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
    <description>creates a matrix of interactions</description>
    <macros>
        <token name="@BINARY@">hicBuildMatrix</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[

        hicBuildMatrix

            --samFiles
            #for $repeat in $samFiles:
                '${repeat.samFile}'
            #end for

            #if $binSize and $binSize is not None:
                --binSize $binSize
            #end if

            #if $fragmentLength and $fragmentLength is not None:
                --fragmentLength $fragmentLength
            #end if

            #if $restrictionCutFile and $restrictionCutFile is not None:
                --restrictionCutFile $restrictionCutFile
            #end if

            #if $minDistance and $minDistance is not None:
                --minDistance $minDistance
            #end if

            #if $maxDistance and $maxDistance is not None:
                --maxDistance $maxDistance
            #end if

            #if $restrictionSequence and $restrictionSequence is not None:
                --restrictionSequence '$restrictionSequence'
            #end if

            #if $region and $region is not None:
                --region '$region'
            #end if

            --outFileName ./numpy_array.npz
            --outBam ./unsorted.bam

            #if $restrictionCutFile:
                --restrictionCutFile '$restrictionCutFile'
            #end if

            $removeSelfCircles

            #if $minMappingQuality
                --minMappingQuality $minMappingQuality
            #end if
        &&

        samtools sort ./unsorted.bam -o sorted.bam

]]>
    </command>
    <inputs>
        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">
            <param name="samFile" type="data" format="sam,bam"/>
        </repeat>

        <param argument="--restrictionCutFile" type="data" format="bed" optional="True"
            help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
                  bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>

        <param name="binSize" type="integer" value="10000" label="Bin size in bp"
            help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
            Otherwise all reads in the interval are considered. " argument="--binSize"/>

        <param name="fragmentLength" type="integer" value="300" optional="true" label="Estimated fragment length" argument="--fragmentLength" />

        <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
            help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments
            (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/>

        <param name="minDistance" type="integer" value="300" optional="true" label="Minimum distance between restriction sites"
            help="Restriction sites that are closer that this distance are merged into one.
            This option only applies if --restrictionCutFile is given." argument="--minDistance"/>

        <param name="maxDistance" type="integer" value="800" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one"
            help="This option only applies if --restrictionCutFile is given."  argument="--maxDistance"/>

        <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
            help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
            &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/>

        <expand macro="region" />

        <param argument="--removeSelfCircles" type="boolean" truevalue="--removeSelfCircles" falsevalue=""
            label="Save the matrix of values underlying the heatmap" help="If set, outward facing reads, at a distance of less thatn 25kbs are removed." />

        <expand macro="minMappingQuality" />


    </inputs>
    <outputs>
        <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
        <data name="outFileName" from_work_dir="numpy_array.npz.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <repeat name="samFiles">
                <param name="samFile" value="r1.sam" ftype="sam" />
            </repeat>
            <repeat name="samFiles">
                <param name="samFile" value="r2.sam" ftype="sam"/>
            </repeat>
            <param name="binSize" value="10000"/>
            <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/>
            <output name="outFileName" file="hicBuildMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

Creates a matrix of interactions

]]></help>
    <expand macro="citations" />
</tool>