comparison deepTools_macros.xml @ 65:9bee2c86eeb1 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty

64:627004611e98

            <when value="no" />
            <when value="yes">
                <expand macro="doNotExtendPairedEnds" />
                <expand macro="ignoreDuplicates" />
                <expand macro="minMappingQuality" />
                <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
                    label="Include zeros"
                    help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" />
                <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
                    help="If not specified the value is set automatically. (--zMin)"/>
                <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
                    help="If not specified the value is set automatically. (--zMax)"/>
                <expand macro="colormap" />
            </when>
        </conditional>
    </xml>

    <xml name="region_limit_operation">
        <param name="region" type="text" value=""
            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;. (--region)" />
    </xml>
    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">1.5.9.2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" >deepTools</requirement>
            <requirement type="package" version="1.5.9">deepTools</requirement>
            <yield />
        </requirements>
        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="kmeans_clustering">
        <conditional name="used_multiple_regions">

                #end if
            #end if
        #end if
    </token>

    <xml name="doNotExtendPairedEnds">
        <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
            label="Do not extend paired ends"
            help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
    </xml>

.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://github.com/fidelram/deepTools/wiki/

**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite the following paper:

    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gku365</citation>
            <yield />

                label="Bam file" 
                help="The BAM file must be sorted."/>
            <param name="label" type="text" size="30" optional="true" value=""
                label="Label"
                help="Label to use in the output. If not given the dataset name will be used instead."/>
          </repeat>
    </xml>

    <token name="@multiple_input_bams@">
        #import tempfile
        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())

            ##set $files += [str($i.bamfile)]
            #if str($i.label.value) != "":
                #set $labels += ["\"%s\"" % ($i.label.value)]
            #else
                #set $labels += ["\"%s\"" % ($i.bamfile.name)]
            #end if
        #end for
    </token>

    <xml name="reference_genome_source">

65:9bee2c86eeb1

            <when value="no" />
            <when value="yes">
                <expand macro="doNotExtendPairedEnds" />
                <expand macro="ignoreDuplicates" />
                <expand macro="minMappingQuality" />
                <expand macro="includeZeros" />
                <expand macro="zMin_zMax" />
                <expand macro="colormap" />
            </when>
        </conditional>
    </xml>


    <xml name="bigwigCorrelate_mode_actions">

        <expand macro="region_limit_operation" />

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="includeZeros" />
                <expand macro="zMin_zMax" />
                <expand macro="colormap" />
                <expand macro="plotTitle" />
                <expand macro="plotNumbers" />
            </when>
        </conditional>
    </xml>


    <xml name="includeZeros">
        <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
            label="Include zeros"
            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" />
    </xml>
    <xml name="zMin_zMax">
        <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
            help="If not specified the value is set automatically. (--zMin)"/>
        <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
            help="If not specified the value is set automatically. (--zMax)"/>
    </xml>

    <xml name="region_limit_operation">
        <param name="region" type="text" value=""
            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;. (--region)" />
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">1.5.9.2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" >deepTools</requirement>
            <requirement type="package" version="1.5.9">deepTools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="kmeans_clustering">
        <conditional name="used_multiple_regions">

                #end if
            #end if
        #end if
    </token>

    <xml name="samFlag">
        <param name="samFlag" type="integer" optional="true" value=""
            label="Filter reads based on the SAM flag"
            help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
    </xml>
    <xml name="plotNumbers">
        <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 
            label="Plot the correlation value" 
            help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
    </xml>
    <xml name="doNotExtendPairedEnds">
        <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
            label="Do not extend paired ends"
            help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/>
    </xml>

.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://github.com/fidelram/deepTools/wiki/

    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gku365</citation>
            <yield />

                label="Bam file" 
                help="The BAM file must be sorted."/>
            <param name="label" type="text" size="30" optional="true" value=""
                label="Label"
                help="Label to use in the output. If not given the dataset name will be used instead."/>
        </repeat>
    </xml>

    <xml name="multiple_input_bigwigs">
        <repeat name="input_files" title="BigWig files" min="2">
            <param name="bigwigfile" type="data" format="bigwig" 
                label="Bigwig file" 
                help="The Bigwig file must be sorted."/>
            <param name="label" type="text" size="30" optional="true" value=""
                label="Label"
                help="Label to use in the output. If not given the dataset name will be used instead."/>
        </repeat>
    </xml>

    <xml name="plotTitle">
        <param name="plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"
            help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
    </xml>

    <token name="@multiple_input_bams@">
        #import tempfile
        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())

            ##set $files += [str($i.bamfile)]
            #if str($i.label.value) != "":
                #set $labels += ["\"%s\"" % ($i.label.value)]
            #else
                #set $labels += ["\"%s\"" % ($i.bamfile.name)]
            #end if
        #end for
    </token>

    <token name="@multiple_input_bigwigs@">
        #import tempfile
        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
        #set files=[]
        #set labels=[]
        #for $i in $input_files:
            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
            #set $temp_input_path = $temp_input_handle.name
            #silent $temp_input_handle.close()
            #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
            #silent $files.append('%s.bw' % $temp_input_path)

            ##set $files += [str($i.bigwigfile)]
            #if str($i.label.value) != "":
                #set $labels += ["\"%s\"" % ($i.label.value)]
            #else
                #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
            #end if
        #end for
    </token>

    <xml name="reference_genome_source">