comparison deepTools_macros.xml @ 70:a4bbac56f046 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty

69:0eb2441d1fcf

            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams">
        <repeat name="input_files" title="BAM files" min="2">
            <param name="bamfile" type="data" format="bam" 
                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" 

    <token name="@multiple_input_bams@">
        #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 $temp_input_handle.close()
            #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
            #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
            #silent $files.append('%s.bam' % $temp_input_path)

            ##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

70:a4bbac56f046

            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams">
        <param name="bamfiles" type="data" format="bam"
            label="Bam file" multiple="true"
            help="The BAM file must be sorted."/>
    </xml>

    <xml name="multiple_input_bigwigs">
        <repeat name="input_files" title="BigWig files" min="2">
            <param name="bigwigfile" type="data" format="bigwig" 

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

            #silent $labels.append("\"%s\"" % ($i.name))
        #end for
    </token>

    <token name="@multiple_input_bigwigs@">
        #import tempfile