comparison bamCompare.xml @ 8:89f6d2283317 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe

7:d5d57b40b29a

                $advancedOpt.skipNAs

                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                    --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
                #end if
            #end if
]]>
    </command>
    <inputs>
        <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"

        <conditional name="comparison">
            <param name="type" type="select"
                label="How to compare the two files"
                help="The default is to output the log2ratio between the two samples.
                The reciprocal ratio returns the negative of the inverse of the ratio if
                the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
                <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
                <option value="ratio">Compute the ratio of the number of reads</option>
                <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
                <option value="add">Compute the sum of number of reads</option>
                <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
            </param>
            <when value="log2">
                <expand macro="pseudocount" />
            </when>
            <when value="ratio">
                <expand macro="pseudocount" />
            </when>
            <when value="add" />
            <when value="reciprocal_ratio">
                <expand macro="pseudocount" />
            </when>
            <when value="subtract">
                <conditional name="normalization">

            <when value="yes">
                <expand macro="smoothLength" />
                <expand macro="read_processing_options" />

                <expand macro="skipNAs" />
                <param argument="--ignoreForNormalization" type="text" value="" size="50"
                    label="regions that should be excluded for calculating the scaling factor"
                    help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
                        For example, if you know of copy number variations between samples then you may want to exclude these.
                        Another typical example is the difference in chromosome X copies between males and females in many species.
                        Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bigwig" name="outFileName">

8:89f6d2283317

                $advancedOpt.skipNAs

                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                    --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
                #end if

                @blacklist@
            #end if
]]>
    </command>
    <inputs>
        <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"

        <conditional name="comparison">
            <param name="type" type="select"
                label="How to compare the two files"
                help="The default is to output the log2ratio between the two samples.
                The reciprocal ratio returns the negative of the inverse of the ratio if
                the ratio is less than 0. The resulting values are interpreted as negative
                fold changes. To output the scaled values from the first or second BAM file,
                select 'first' or 'second'.">
                <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
                <option value="ratio">Compute the ratio of the number of reads</option>
                <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
                <option value="add">Compute the sum of number of reads</option>
                <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
                <option value="first">Returns the scaled value of the first BAM file</option>
                <option value="second">Returns the scaled value of the second BAM file</option>
            </param>
            <when value="log2">
                <expand macro="pseudocount" />
            </when>
            <when value="ratio">
                <expand macro="pseudocount" />
            </when>
            <when value="add" />
            <when value="first" />
            <when value="second" />
            <when value="reciprocal_ratio">
                <expand macro="pseudocount" />
            </when>
            <when value="subtract">
                <conditional name="normalization">

            <when value="yes">
                <expand macro="smoothLength" />
                <expand macro="read_processing_options" />

                <expand macro="skipNAs" />

                <param argument="--ignoreForNormalization" type="text" value="" size="50"
                    label="regions that should be excluded for calculating the scaling factor"
                    help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
                        For example, if you know of copy number variations between samples then you may want to exclude these.
                        Another typical example is the difference in chromosome X copies between males and females in many species.
                        Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />
                <expand macro="blacklist" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bigwig" name="outFileName">