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comparison deseq2.xml @ 2:afe2a77c5900 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
author iuc
date Wed, 02 Dec 2015 17:40:45 -0500
parents 89bbd1dbf48d
children 248e9c78346e
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1:89bbd1dbf48d 2:afe2a77c5900
1 <tool id="deseq2" name="DESeq2" version="2.1.8.2"> 1 <tool id="deseq2" name="DESeq2" version="2.1.8.3">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <requirements> 3 <requirements>
4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> 4 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
5 <requirement type="package" version="1.8.2">deseq2</requirement> 5 <requirement type="package" version="1.8.2">deseq2</requirement>
6 </requirements> 6 </requirements>
39 #for $file in $level.countsFile: 39 #for $file in $level.countsFile:
40 $count_files.append(str($file)) 40 $count_files.append(str($file))
41 #end for 41 #end for
42 $temp_factor.append( {str($level.factorLevel): $count_files} ) 42 $temp_factor.append( {str($level.factorLevel): $count_files} )
43 #end for 43 #end for
44 $temp_factor.reverse()
44 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 45 $temp_factor_names.append([str($factor.factorName), $temp_factor])
45 #end for 46 #end for
46 -f '#echo json.dumps(temp_factor_names)#' 47 -f '#echo json.dumps(temp_factor_names)#'
47 -t "$fit_type" 48 -t "$fit_type"
48 #if $outlier_replace_off: 49 #if $outlier_replace_off:
168 ------ ---------------------------------------------------------- 169 ------ ----------------------------------------------------------
169 1 Gene Identifiers 170 1 Gene Identifiers
170 2 mean normalised counts, averaged over all samples from both conditions 171 2 mean normalised counts, averaged over all samples from both conditions
171 3 the logarithm (to basis 2) of the fold change (See the note in inputs section) 172 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
172 4 standard error estimate for the log2 fold change estimate 173 4 standard error estimate for the log2 fold change estimate
173 5 p value for the statistical significance of this change 174 5 Wald statistic
174 6 p value adjusted for multiple testing with the Benjamini-Hochberg procedure 175 6 p value for the statistical significance of this change
176 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
175 which controls false discovery rate (FDR) 177 which controls false discovery rate (FDR)
176 ====== ========================================================== 178 ====== ==========================================================
177 179
178 180
179 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html 181 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html