comparison hicBuildMatrix.xml @ 15:231687cac31b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"

14:76b189fd277b

                --minDistance $restrictionCutFileBinSize_conditional.minDistance
                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
            #end if

            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
                --binSize 
                #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
                    '${repeat.binSize}'
                #end for
            #end if

        #end if

]]>
    </command>
    <inputs>
        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" 
                help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
            <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
        </repeat>
        <conditional name="restrictionCutFileBinSize_conditional">
            <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">

        <expand macro="minMappingQuality" />

        <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
            help="Sequence left by the restriction enzyme after cutting.
                    Each restriction enzyme recognizes a different DNA sequence and, 
                    after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. 
                    For DpnII, the restriction site and dangling end sequence are the same: GATC. 
                    This information is easily found on the description of the restriction enzyme.
                    The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>

        <param name='outBam_Boolean' type='boolean' truevalue='--outBam'  falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file"

15:231687cac31b

                --minDistance $restrictionCutFileBinSize_conditional.minDistance
                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
            #end if

            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
                --binSize
                #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
                    '${repeat.binSize}'
                #end for
            #end if

        #end if

]]>
    </command>
    <inputs>
        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)"
                help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
            <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
        </repeat>
        <conditional name="restrictionCutFileBinSize_conditional">
            <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">

        <expand macro="minMappingQuality" />

        <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
            help="Sequence left by the restriction enzyme after cutting.
                    Each restriction enzyme recognizes a different DNA sequence and,
                    after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
                    For DpnII, the restriction site and dangling end sequence are the same: GATC.
                    This information is easily found on the description of the restriction enzyme.
                    The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>

        <param name='outBam_Boolean' type='boolean' truevalue='--outBam'  falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file"