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comparison computeMatrix.xml @ 10:a68a771625d2 draft

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author bgruening
date Tue, 29 Oct 2013 17:26:28 -0400
parents 73761f33f198
children 8436c195dd6c
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9:73761f33f198 10:a68a771625d2
1 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0"> 1 <tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0">
2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description> 2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
3 <requirements> 3 <expand macro="requirements" />
4 <requirement type="package" version="1.5.1_3e13687c89e951476776b15afb4bbbc3b906f761">deepTools</requirement> 4 <macros>
5 <requirement type="package" >deepTools</requirement> 5 <import>deepTools_macros.xml</import>
6 </requirements> 6 </macros>
7 <command> 7 <command>
8 #import tempfile 8 #import tempfile
9 9
10 #set $temp_input_handle = tempfile.NamedTemporaryFile() 10 #set $temp_input_handle = tempfile.NamedTemporaryFile()
11 #set $temp_input_path = $temp_input_handle.name 11 #set $temp_input_path = $temp_input_handle.name
12 #silent $temp_input_handle.close() 12 #silent $temp_input_handle.close()
13 13
26 $mode.mode_select 26 $mode.mode_select
27 --regionsFileName '$temp_input_path' 27 --regionsFileName '$temp_input_path'
28 --scoreFileName '$scoreFile' 28 --scoreFileName '$scoreFile'
29 --outFileName '$outFileName' 29 --outFileName '$outFileName'
30 30
31 --numberOfProcessors 4 31 @THREADS@
32 32
33 #if $output.showOutputSettings == "yes" 33 #if $output.showOutputSettings == "yes"
34 #if $output.saveData: 34 #if $output.saveData:
35 --outFileNameData '$outFileNameData' 35 --outFileNameData '$outFileNameData'
36 #end if 36 #end if
206 <param name="mode.afterRegionStartLength" value="100" /> 206 <param name="mode.afterRegionStartLength" value="100" />
207 <output name="outFileName" file="master.mat.gz" ftype="bgzip" compare="sim_size" delta="100" /> 207 <output name="outFileName" file="master.mat.gz" ftype="bgzip" compare="sim_size" delta="100" />
208 </test> 208 </test>
209 </tests> 209 </tests>
210 <help> 210 <help>
211
211 **What it does** 212 **What it does**
212 213
213 This tool summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile. Typically, these genomic regions are genes, but any other regions defined in a BED or INTERVAL format can be used. This tool can also be used to filter and sort regions according to their score. 214 This tool summarizes and prepares an intermediary file
215 containing scores associated with genomic regions that can be used
216 afterwards to plot a heatmap or a profile.
217
218 Genomic regions can really be anything - genes, parts of genes, ChIP-seq
219 peaks, favorite genome regions... as long as you provide a proper file
220 in BED or INTERVAL format. This tool can also be used to filter and sort
221 regions according to their score.
222
223
224 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
225 :alt: Relationship between computeMatrix, heatmapper and profiler
226
214 227
215 ----- 228 -----
216 229
217 .. class:: infomark 230 .. class:: infomark
218 231
219 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com 232 @REFERENCES@
220 233
221 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. 234 </help>
222
223 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
224 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
225 </help>
226 </tool> 235 </tool>