comparison bamCompare.xml @ 22:59cbb059cd1e draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d

21:e4287c038599

                    --smoothLength '$advancedOpt.smoothLength'
                #end if

                @ADVANCED_OPTS_READ_PROCESSING@
                $advancedOpt.skipNAs

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

            <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.

22:59cbb059cd1e

                    --smoothLength '$advancedOpt.smoothLength'
                #end if

                @ADVANCED_OPTS_READ_PROCESSING@
                $advancedOpt.skipNAs
                $advancedOpt.skipZeroOverZero

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

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

                <expand macro="skipNAs" />
                <param argument="--skipZeroOverZero" type="select" label="Skip bins of no coverage"
                    help="Skip bins where BOTH files lack coverage.">
                    <option value="no" selected="true">No</option>
                    <option value="yes">Yes, skip them.</option>
                </param>

                <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.