comparison computeMatrix.xml @ 8:e3f4303309cc draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7

7:021729469baf

                help="File, in BED format, containing the regions to plot."/>
        </repeat>

        <param name="scoreFileName" format="bigwig" type="data"
            label="Score file" multiple="True"
            help="Should be a bigWig file (containing a score, usually covering
            the whole genome). You can generate a bigWig file either from a
            bedGraph or WIG file using UCSC tools or from a BAM file using the
            deepTool bamCoverage. (--scoreFileName)"/>

        <conditional name="mode" >
            <param name="mode_select" type="select"
                label="computeMatrix has two main output options"
                help="In the scale-regions mode, all regions in the BED file are
                stretched or shrunk to the same length (bp) that is indicated
                by the user. Reference-point refers to a position within the BED
                regions (e.g start of region). In the reference-point mode only
                those genomic positions before (downstream) and/or after (upstream)
                the reference point will be considered.">
                <option value="scale-regions" selected="true">scale-regions</option>
                <option value="reference-point">reference-point</option>
            </param>

            <when value="scale-regions" >
                <param argument="--regionBodyLength" type="integer" value="500"
                    label="Distance in bp to which all regions are going to be fitted" help=""/>
                <conditional name="regionStartLength">
                    <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
                        <option value="no" selected="true">no</option>
                        <option value="yes">yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
                            label="Distance upstream of the start site of the regions defined in the region file"
                            help="If the regions are genes, this would be the
                            distance upstream of the transcription start site."/>
                        <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
                            label="Distance downstream of the end site of the given regions"
                            help="If the regions are genes, this would be the
                            distance downstream of the transcription end site."/>
                    </when>
                </conditional>
            </when>

                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="binSize" type="integer" value="50" min="1"
                    label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length"
                    help="(--binSize)"/>

                <expand macro="sortRegions" />
                <expand macro="sortUsing" />

    </tests>
  <help>
<![CDATA[
**What it does**

This tool prepares an intermediary file (a gzipped table of values)
that contains scores associated with genomic regions that can be used
afterwards to plot a heatmap or a profile.

Genomic regions can really be anything - genes, parts of genes, ChIP-seq
peaks, favorite genome regions... as long as you provide a proper file
in BED or INTERVAL format. If you would like to compare different groups of regions
(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.

8:e3f4303309cc

                help="File, in BED format, containing the regions to plot."/>
        </repeat>

        <param name="scoreFileName" format="bigwig" type="data"
            label="Score file" multiple="True"
            help="You can generate a bigWig file from either a
            bedGraph or WIG file using UCSC tools or from a BAM file using the
            bamCoverage tool. (--scoreFileName)"/>

        <conditional name="mode" >
            <param name="mode_select" type="select"
                label="computeMatrix has two main output options"
                help="In the scale-regions mode, all regions in the BED file are
                stretched or shrunk to the same length (in bases) that is indicated
                by the user. Reference-point refers to a position within the BED
                regions (e.g start of region). In the reference-point mode only
                those genomic positions before (upstream) and/or after (downstream)
                the reference point will be considered.">
                <option value="scale-regions" selected="true">scale-regions</option>
                <option value="reference-point">reference-point</option>
            </param>

            <when value="scale-regions" >
                <param argument="--regionBodyLength" type="integer" value="500"
                    label="Distance in bases to which all regions are going to be fit" help=""/>
                <conditional name="regionStartLength">
                    <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
                        <option value="no" selected="true">no</option>
                        <option value="yes">yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
                            label="Distance upstream of the region start position"
                            help="If the regions are genes, this would be the
                            distance upstream of the transcription start site."/>
                        <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
                            label="Distance downstream of the region end position"
                            help="If the regions are genes, this would be the
                            distance downstream of the transcription end site."/>
                    </when>
                </conditional>
            </when>

                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="binSize" type="integer" value="50" min="1"
                    label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length"
                    help="(--binSize)"/>

                <expand macro="sortRegions" />
                <expand macro="sortUsing" />

    </tests>
  <help>
<![CDATA[
**What it does**

This tool prepares an intermediate file (a gzipped table of values)
that contains scores associated with genomic regions and can be used
afterwards to plot a heatmap or profile.

Genomic regions can really be anything - genes, parts of genes, ChIP-seq
peaks, favorite genome regions... as long as you provide a proper file
in BED or INTERVAL format. If you would like to compare different groups of regions
(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.