comparison deepTools_macros.xml @ 14:d4fdd10516f6 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28

13:b8431744eab3

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.5.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>

            <when value="no" />
            <when value="yes">
                <yield/>
            </when>
        </conditional>
    </xml>

    <token name="@ADVANCED_OPTS_READ_PROCESSING@">
        #if $advancedOpt.doExtendCustom.doExtend == 'custom':
            --extendReads $advancedOpt.doExtendCustom.extendReadsValue

            <citation type="doi">10.1093/nar/gkw257</citation>
            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams">
        <conditional name="multibam_conditional">
        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bamfiles" type="data" format="bam" min="1"
                label="Bam file" multiple="true"
                help=""/>
        </when>
        <when value="Yes">
            <repeat name="multibam_repeats" min="1" title="BAM Files">
                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="multiple_input_bams_min2">
        <conditional name="multibam_conditional">
        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bamfiles" type="data" format="bam" min="2"
                label="Bam file" multiple="true"
                help=""/>
        </when>
        <when value="Yes">
            <repeat name="multibam_repeats" min="2" title="BAM Files">
                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="multiple_input_bigwigs">
        <conditional name="multibigwig_conditional">
        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
                label="Bigwig file"
                help="A Bigwig file."/>
        </when>
        <when value="Yes">
            <repeat name="multibigwig_repeats" min="2" title="BigWig files">
                <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
            </repeat>
        </when>
        </conditional>
    </xml>

        #set files=[]
        #set labels=[]
        #import re
        #if $multibigwig_conditional.orderMatters == "No":
            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
            #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                ln -s "${bigwig}" "${counter}.bw" &&
                #silent $files.append('%s.bw' % $counter)
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                ln -s "${f.bigwigfiles}" "${counter}.bw" &&
                #silent $files.append('%s.bw' % $counter)
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #end if
]]>
    </token>

14:d4fdd10516f6

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.5.1.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>

            <when value="no" />
            <when value="yes">
                <yield/>
            </when>
        </conditional>
    </xml>

    <token name="@PLOTWIDTHHEIGHT@">
        --plotWidth '$advancedOpt.plotWidth'
        --plotHeight '$advancedOpt.plotHeight'
    </token>

    <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
        <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
            label="Plot height"
            help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />

        <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
            label="Plot width"
            help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
    </xml>

    <token name="@ADVANCED_OPTS_READ_PROCESSING@">
        #if $advancedOpt.doExtendCustom.doExtend == 'custom':
            --extendReads $advancedOpt.doExtendCustom.extendReadsValue

            <citation type="doi">10.1093/nar/gkw257</citation>
            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams" tokens="MIN">
        <conditional name="multibam_conditional">
        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bamfiles" type="data" format="bam" min="@MIN@"
                label="Bam file" multiple="true"
                help=""/>
        </when>
        <when value="Yes">
            <repeat name="multibam_repeats" min="@MIN@" title="BAM Files">
                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
        <conditional name="multibigwig_conditional">
        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
                label="@LABEL@"
                help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
        </when>
        <when value="Yes">
            <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
            </repeat>
        </when>
        </conditional>
    </xml>

        #set files=[]
        #set labels=[]
        #import re
        #if $multibigwig_conditional.orderMatters == "No":
            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #end if
]]>
    </token>