Mercurial > repos > bgruening > deeptools

comparison computeMatrix.xml @ 5:1f312af2f8db draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 06 Aug 2013 08:20:47 -0400
parents c8a0dc481493
children c5847db0cb41
comparison
equal deleted inserted replaced
4:c8a0dc481493 5:1f312af2f8db
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 <requirements>
4 <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement> 4 <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 #import tempfile
8
9 #set $temp_input_handle = tempfile.NamedTemporaryFile()
10 #set $temp_input_path = $temp_input_handle.name
11 #silent $temp_input_handle.close()
12
13 #for $rf in $regionsFiles:
14 cat "$rf.regionsFile" >> $temp_input_path;
15 #if str($rf.label.value).strip():
16 echo "\#$rf.label.value" >> $temp_input_path;
17 #else:
18 echo "\#$rf.regionsFile.name" >> $temp_input_path;
19 #end if
20 #end for
21
22
7 computeMatrix 23 computeMatrix
8 24
9 $mode.mode_select 25 $mode.mode_select
10 --regionsFileName '$regionsFile' 26 --regionsFileName '$temp_input_path'
11 --scoreFileName '$scoreFile' 27 --scoreFileName '$scoreFile'
12 --outFileName '$outFileName' 28 --outFileName '$outFileName'
13 29
14 ##ToDo
15 --numberOfProcessors 4 30 --numberOfProcessors 4
16 31
17 #if $output.showOutputSettings == "yes" 32 #if $output.showOutputSettings == "yes"
18 #if $output.saveData: 33 #if $output.saveData:
19 --outFileNameData '$outFileNameData' 34 --outFileNameData '$outFileNameData'
59 #if $advancedOpt.scale: 74 #if $advancedOpt.scale:
60 --scale $advancedOpt.scale 75 --scale $advancedOpt.scale
61 #end if 76 #end if
62 77
63 #end if 78 #end if
79 ; rm $temp_input_path
64 80
65 </command> 81 </command>
66 <inputs> 82 <inputs>
67 <param name="regionsFile" format="bed,gff" type="data" label="Regions to plot" help="File, in BED or GFF format, containing the regions to plot."/> 83
68 <param name="scoreFile" format="bigwig,bam" type="data" label="Score file" help="Either a bigWig file (containing a score, usually covering the whole genome) or a BAM file. For this last case, coverage counts will be used for the heatmap."/> 84 <repeat name="regionsFiles" title="regions to plot" min="1">
85 <param name="regionsFile" format="bed" type="data" label="Regions to plot" help="File, in BED or GFF format, containing the regions to plot."/>
86 <param name="label" type="text" size="30" optional="true" value="" label="Label" help="Label to use in the output."/>
87 </repeat>
88
89 <param name="scoreFile" format="bigwig" type="data" label="Score file" help="Either a bigWig file (containing a score, usually covering the whole genome) or a BAM file. For this last case, coverage counts will be used for the heatmap."/>
69 90
70 <conditional name="mode" > 91 <conditional name="mode" >
71 <param name="mode_select" type="select" label="computeMatrix has two main output options" help="In the scale-regions mode, all regions in the BED/GFF 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/GFF 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 plotted."> 92 <param name="mode_select" type="select" label="computeMatrix has two main output options" help="In the scale-regions mode, all regions in the BED/GFF 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/GFF 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 plotted.">
72 <option value="scale-regions" selected="true">scale-regions</option> 93 <option value="scale-regions" selected="true">scale-regions</option>
73 <option value="reference-point">reference-point</option> 94 <option value="reference-point">reference-point</option>