comparison plotEnrichment.xml @ 4:8980933fd546 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

3:c1bc2d0c2e5b

        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[

        @multiple_input_bams@
        @BINARY@
            @THREADS@

            --plotFile '$outFileName'

                --numPlotsPerRow '$advancedOpt.numPlotsPerRow'

                --alpha '$advancedOpt.alpha'

                @ADVANCED_OPTS_READ_PROCESSING@

                @blacklist@

                $advancedOpt.keepExons

            <expand macro="read_processing_options" />

            <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
                label="Include BED12 exons"
                help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />

            <expand macro="blacklist" />

        </expand>

4:8980933fd546

        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        @multiple_input_bams@
        @BINARY@
            @THREADS@

            --plotFile '$outFileName'

                --numPlotsPerRow '$advancedOpt.numPlotsPerRow'

                --alpha '$advancedOpt.alpha'

                @ADVANCED_OPTS_READ_PROCESSING@

                #if $advancedOpt.Offset:
                    --Offset $advancedOpt.Offset
                #end if

                @blacklist@

                $advancedOpt.keepExons

            <expand macro="read_processing_options" />

            <param argument="--keepExons" type="boolean" truevalue="--keepExons" falsevalue=""
                label="Include BED12 exons"
                help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." />

            <param argument="--Offset" type="text"  value="" optional="True"
                label="Offset inside each alignment to use for the signal location."
                help="Uses this offset inside of each read as the signal. This is useful in
                    cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned
                    should be used to denote where the signal is (rather than the span of the
                    whole alignment). This can be paired with the --filterRNAstrand option. Note
                    that negative values indicate offsets from the end of each read. A value of
                    1 indicates the first base of the alignment (taking alignment orientation
                    into account). Likewise, a value of -1 is the last base of the alignment. An
                    offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be
                    used to specify a range of positions. Note that specifying something like
                    --Offset 5 -1 will result in the 5th through last position being used, which
                    is equivalent to trimming 4 bases from the 5-prime end of alignments." />

            <expand macro="blacklist" />

        </expand>