comparison bamCoverage.xml @ 10:aa33302db115 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09

9:e22b1110529c

                #if str($advancedOpt.filterRNAstrand) != 'no':
                    --filterRNAstrand '$advancedOpt.filterRNAstrand'
                #end if

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

                @blacklist@
            #end if
]]>

                <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
                    label="Determine nucleosome positions from MNase-seq data"
                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options." />

                <param argument="--Offset" type="integer"  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. By default, the entire alignment is used to
                        denote where the signal is located." />

                <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
                    help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
                          Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
                    <option value="no" selected="true">no</option>

            <param name="showAdvancedOpt" value="yes" />
            <param name="filterRNAstrand" value="reverse" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
        </test>
    </tests>
    <help>
<![CDATA[

What it does

10:aa33302db115

                #if str($advancedOpt.filterRNAstrand) != 'no':
                    --filterRNAstrand '$advancedOpt.filterRNAstrand'
                #end if

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

                @blacklist@
            #end if
]]>

                <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
                    label="Determine nucleosome positions from MNase-seq data"
                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options." />

                <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." />

                <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." 
                    help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
                          Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
                    <option value="no" selected="true">no</option>

            <param name="showAdvancedOpt" value="yes" />
            <param name="filterRNAstrand" value="reverse" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
        </test>
        <test>
            <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" />
            <param name="outFileFormat" value="bigwig" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="binSize" value="10" />
            <param name="Offset" value="-4 -1" />
            <param name="doExtend" value="yes" />
            <param name="minMappingQuality" value="0" />
            <param name="type" value="no" />
            <output name="outFileName" file="bamCoverage_result6.bw" ftype="bigwig" />
        </test>
    </tests>
    <help>
<![CDATA[

What it does