comparison deepTools_macros.xml @ 42:0d2ba04b8261 draft default tip

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9

41:a4ecef241a6d

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.5.1.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.5.1">deeptools</requirement>
            <requirement type="package" version="1.9">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

    </xml>

    <xml name="pseudocount">
        <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
    </xml>

    <token name="@REFERENCES@">

.. class:: infomark

For more information on the tools, please visit our `help site`_.

    <token name="@multiple_input_bams@">
<![CDATA[
        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
            #set custom_labels=labels
        #end if
        #set files=[]
        #set labels=[]
        #import re
        #if $multibam_conditional.orderMatters == "No":

                    ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
                #else:
                    ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                #end if
                #silent $files.append("'%s.bam'" % $counter)
                #silent $labels.append("'%s'" % identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                ln -s '${f.bamfiles}' './${counter}.bam' &&

    </token>

    <token name="@multiple_input_bigwigs@">
<![CDATA[
        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
            #set custom_labels=labels
        #end if
        #set files=[]
        #set labels=[]
        #import re
        #if $multibigwig_conditional.orderMatters == "No":

42:0d2ba04b8261

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@TOOL_VERSION@">3.5.2</token>
    <token name="@GALAXY_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
            <requirement type="package" version="1.9">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

    </xml>

    <xml name="pseudocount">
        <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
    </xml>
    <token name="@REFERENCES@">

.. class:: infomark

For more information on the tools, please visit our `help site`_.

    <token name="@multiple_input_bams@">
<![CDATA[
        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
            #set custom_labels=$custom_sample_labels_conditional.labels
        #end if
        #set files=[]
        #set labels=[]
        #import re
        #if $multibam_conditional.orderMatters == "No":

                    ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
                #else:
                    ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                #end if
                #silent $files.append("'%s.bam'" % $counter)
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                ln -s '${f.bamfiles}' './${counter}.bam' &&

    </token>

    <token name="@multiple_input_bigwigs@">
<![CDATA[
        #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
            #set custom_labels=$custom_sample_labels_conditional.labels
        #end if
        #set files=[]
        #set labels=[]
        #import re
        #if $multibigwig_conditional.orderMatters == "No":