comparison multiBigwigSummary.xml @ 28:d580d6acd1df draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5

27:459cfa861f0b

<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.0">
    <description>calculates average scores for a list of two or more bigwig files</description>
    <macros>
        <token name="@BINARY@">multiBigwigSummary</token>
        <import>deepTools_macros.xml</import>
    </macros>
   <expand macro="requirements" />
    <command>
<![CDATA[
        #set files=[]
        #set labels=[]

        @multiple_input_bigwigs@

        @BINARY@
            $mode.modeOpt

            @THREADS@

            --outFileName $outFile

            --bwfiles #echo ' '.join($files)#
            --labels #echo ' '.join($labels)#

            #if $outRawCounts:
                --outRawCounts '$outFileRawCounts'
            #end if

            #if $mode.modeOpt == "bins":

                @ADVANCED_OPTS_GTF@
                @blacklist@
            #end if
]]>
    </command>

    <inputs>
        <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/>
        <expand macro="custom_sample_labels" />

        <conditional name="mode">

                <param name="region_file" type="data" format="bed,gtf"
                    label="Region file in BED format"
                    help="Correlation is computed for the number of reads that overlap such regions."/>
            </when>
        </conditional>

        <expand macro="region_limit_operation" />
        <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>

        <expand macro="advancedOpt_scaffold">
            <expand macro="gtf_options" />

    <tests>
        <test>
            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
            <param name="modeOpt" value="bins" />
            <param name="binSize" value="10" />
            <param name="corMethod" value="spearman" />
            <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test>
        <!--test>
            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
            <param name="modeOpt" value="BED-file" />
            <param name="region_file" value="multiBamSummary_regions.bed" />
            <param name="corMethod" value="pearson" />
            <param name="outRawCounts" value="True" />
            <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
            <output name="outFileName" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test-->
    </tests>
    <help>
<![CDATA[

What it does

28:d580d6acd1df

<tool id="deeptools_multi_bigwig_summary" name="multiBigwigSummary" version="@WRAPPER_VERSION@.1">
    <description>calculates average scores for a list of two or more bigwig files</description>
    <macros>
        <token name="@BINARY@">multiBigwigSummary</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        #set files=[]
        #set labels=[]

        @multiple_input_bigwigs@
        @BINARY@
            $mode.modeOpt

            @THREADS@

            --outFileName $outFile

            --bwfiles #echo ' '.join($files)#
            
            #if $custom_sample_labels_conditional.custom_labels_select == 'Yes'
                --labels #echo ' '.join($custom_sample_labels_conditional.labels)#
            #end if
            #if $outRawCounts:
                --outRawCounts '$outFileRawCounts'
            #end if

            #if $mode.modeOpt == "bins":

                @ADVANCED_OPTS_GTF@
                @blacklist@
            #end if
]]>
    </command>
    <inputs>
        <expand macro="multiple_input_bigwigs" MIN="2" LABEL="Bigwig files" TITLE="BigWig files"/>
        <expand macro="custom_sample_labels" />

        <conditional name="mode">

                <param name="region_file" type="data" format="bed,gtf"
                    label="Region file in BED format"
                    help="Correlation is computed for the number of reads that overlap such regions."/>
            </when>
        </conditional>
        <expand macro="region_limit_operation" />
        <param argument="--outRawCounts" type="boolean" label="Save raw counts (scores) to file" help=""/>

        <expand macro="advancedOpt_scaffold">
            <expand macro="gtf_options" />

    <tests>
        <test>
            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
            <param name="modeOpt" value="bins" />
            <param name="binSize" value="10" />
            <output name="outFile" file="multiBigwigSummary_result1.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test>
        <test>
            <param name="bigwigfiles" value="test.bw,test.bw" ftype="bigwig" />
            <param name="modeOpt" value="bins" />
            <param name="binSize" value="10" />
            <param name="outRawCounts" value="True" />
            <conditional name="custom_sample_labels_conditional">
                <param name="custom_labels_select" value="Yes"/>
                <param name="labels" value="sample1 sample2"/>
            </conditional>
            <output name="outFileRawCounts" file="multiBigwigSummary_result2.tabular" ftype="tabular" />
            <output name="outFile" file="multiBigwigSummary_result2.npz" ftype="deeptools_coverage_matrix" compare="sim_size" />
        </test>
    </tests>
    <help>
<![CDATA[

What it does