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comparison deseq2.xml @ 18:72613128bd65 draft

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author bgruening
date Mon, 30 Sep 2013 11:15:24 -0400
parents a05999fd6e26
children bbea9c694b34
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17:a05999fd6e26 18:72613128bd65
2 <description>Determines differentially expressed features from count data</description> 2 <description>Determines differentially expressed features from count data</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">Rscript</requirement> 4 <requirement type="binary">Rscript</requirement>
5 <requirement type="R-module">DESeq2</requirement> 5 <requirement type="R-module">DESeq2</requirement>
6 <requirement type="package" version="3.0.1">R_3_0_1</requirement> 6 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
7 <requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement> 7 <requirement type="package" version="1.0.17">deseq2</requirement>
8 <!--<requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement>-->
8 </requirements> 9 </requirements>
9 <command interpreter="Rscript"> 10 <command interpreter="Rscript">
10 #import simplejson 11 #import simplejson
11 deseq2.R 12 deseq2.R
12 -o "$deseq_out" 13 -o "$deseq_out"
18 19
19 -i "$input_matrix" 20 -i "$input_matrix"
20 21
21 #set $temp_factor_name = list() 22 #set $temp_factor_name = list()
22 #for $factor in $rep_factorName: 23 #for $factor in $rep_factorName:
23 #set $temp_factor = dict() 24 #set $temp_factor = dict()
24 #for $level in $factor.rep_factorLevel: 25 #for $level in $factor.rep_factorLevel:
25 ##$temp_factor_list.append( '%s::%s:%s' % ($factor.factorName.replace(' ','_'), $level.factorLevel, $level.factorIndex) ) 26 ##$temp_factor_list.append( '%s::%s:%s' % ($factor.factorName.replace(' ','_'), $level.factorLevel, $level.factorIndex) )
26 $temp_factor.update({str($level.factorLevel): map(int, str($level.factorIndex).split(','))}) 27 $temp_factor.update({str($level.factorLevel): map(int, str($level.factorIndex).split(','))})
27 #end for 28 #end for
28 $temp_factor_name.append([str($factor.factorName), $temp_factor]) 29 $temp_factor_name.append([str($factor.factorName), $temp_factor])