Mercurial > repos > bgruening > deeptools_compute_matrix

comparison computeMatrix.xml @ 8:e3f4303309cc draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
author bgruening
date Wed, 23 Dec 2015 14:44:53 -0500
parents 021729469baf
children d78fdc5e6f37
comparison
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7:021729469baf 8:e3f4303309cc
75 help="File, in BED format, containing the regions to plot."/> 75 help="File, in BED format, containing the regions to plot."/>
76 </repeat> 76 </repeat>
77 77
78 <param name="scoreFileName" format="bigwig" type="data" 78 <param name="scoreFileName" format="bigwig" type="data"
79 label="Score file" multiple="True" 79 label="Score file" multiple="True"
80 help="Should be a bigWig file (containing a score, usually covering 80 help="You can generate a bigWig file from either a
81 the whole genome). You can generate a bigWig file either from a
82 bedGraph or WIG file using UCSC tools or from a BAM file using the 81 bedGraph or WIG file using UCSC tools or from a BAM file using the
83 deepTool bamCoverage. (--scoreFileName)"/> 82 bamCoverage tool. (--scoreFileName)"/>
84 83
85 <conditional name="mode" > 84 <conditional name="mode" >
86 <param name="mode_select" type="select" 85 <param name="mode_select" type="select"
87 label="computeMatrix has two main output options" 86 label="computeMatrix has two main output options"
88 help="In the scale-regions mode, all regions in the BED file are 87 help="In the scale-regions mode, all regions in the BED file are
89 stretched or shrunk to the same length (bp) that is indicated 88 stretched or shrunk to the same length (in bases) that is indicated
90 by the user. Reference-point refers to a position within the BED 89 by the user. Reference-point refers to a position within the BED
91 regions (e.g start of region). In the reference-point mode only 90 regions (e.g start of region). In the reference-point mode only
92 those genomic positions before (downstream) and/or after (upstream) 91 those genomic positions before (upstream) and/or after (downstream)
93 the reference point will be considered."> 92 the reference point will be considered.">
94 <option value="scale-regions" selected="true">scale-regions</option> 93 <option value="scale-regions" selected="true">scale-regions</option>
95 <option value="reference-point">reference-point</option> 94 <option value="reference-point">reference-point</option>
96 </param> 95 </param>
97 96
98 <when value="scale-regions" > 97 <when value="scale-regions" >
99 <param argument="--regionBodyLength" type="integer" value="500" 98 <param argument="--regionBodyLength" type="integer" value="500"
100 label="Distance in bp to which all regions are going to be fitted" help=""/> 99 label="Distance in bases to which all regions are going to be fit" help=""/>
101 <conditional name="regionStartLength"> 100 <conditional name="regionStartLength">
102 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> 101 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
103 <option value="no" selected="true">no</option> 102 <option value="no" selected="true">no</option>
104 <option value="yes">yes</option> 103 <option value="yes">yes</option>
105 </param> 104 </param>
106 <when value="no" /> 105 <when value="no" />
107 <when value="yes"> 106 <when value="yes">
108 <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1" 107 <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1"
109 label="Distance upstream of the start site of the regions defined in the region file" 108 label="Distance upstream of the region start position"
110 help="If the regions are genes, this would be the 109 help="If the regions are genes, this would be the
111 distance upstream of the transcription start site."/> 110 distance upstream of the transcription start site."/>
112 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1" 111 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1"
113 label="Distance downstream of the end site of the given regions" 112 label="Distance downstream of the region end position"
114 help="If the regions are genes, this would be the 113 help="If the regions are genes, this would be the
115 distance downstream of the transcription end site."/> 114 distance downstream of the transcription end site."/>
116 </when> 115 </when>
117 </conditional> 116 </conditional>
118 </when> 117 </when>
145 <option value="yes">yes</option> 144 <option value="yes">yes</option>
146 </param> 145 </param>
147 <when value="no" /> 146 <when value="no" />
148 <when value="yes"> 147 <when value="yes">
149 <param name="binSize" type="integer" value="50" min="1" 148 <param name="binSize" type="integer" value="50" min="1"
150 label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" 149 label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length"
151 help="(--binSize)"/> 150 help="(--binSize)"/>
152 151
153 <expand macro="sortRegions" /> 152 <expand macro="sortRegions" />
154 <expand macro="sortUsing" /> 153 <expand macro="sortUsing" />
155 154
234 </tests> 233 </tests>
235 <help> 234 <help>
236 <![CDATA[ 235 <![CDATA[
237 **What it does** 236 **What it does**
238 237
239 This tool prepares an intermediary file (a gzipped table of values) 238 This tool prepares an intermediate file (a gzipped table of values)
240 that contains scores associated with genomic regions that can be used 239 that contains scores associated with genomic regions and can be used
241 afterwards to plot a heatmap or a profile. 240 afterwards to plot a heatmap or profile.
242 241
243 Genomic regions can really be anything - genes, parts of genes, ChIP-seq 242 Genomic regions can really be anything - genes, parts of genes, ChIP-seq
244 peaks, favorite genome regions... as long as you provide a proper file 243 peaks, favorite genome regions... as long as you provide a proper file
245 in BED or INTERVAL format. If you would like to compare different groups of regions 244 in BED or INTERVAL format. If you would like to compare different groups of regions
246 (i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group. 245 (i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group.