Mercurial > repos > iuc > deseq2

comparison deseq2.xml @ 2:9c706d3721ab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 521ea70d49fee701db4d832823644c8c3050f8f2-dirty
author iuc
date Fri, 04 Sep 2015 07:11:53 -0400
parents 5b1ce9db498e
children 1ae1da9a5e66
comparison
equal deleted inserted replaced
1:522aa36eb845 2:9c706d3721ab
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="3.1.0">R</requirement> 5 <requirement type="package" version="3.1.0">R</requirement>
6 <requirement type="package" version="1.8.1">deseq2</requirement> 6 <requirement type="package" version="1.8.1">deseq2</requirement>
7 </requirements> 7 </requirements>
8 <version_command>
9 <![CDATA[
10 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2) &&
11 cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
12 ]]>
13 </version_command>
8 <command interpreter="Rscript"> 14 <command interpreter="Rscript">
15 <![CDATA[
9 #import json 16 #import json
10 deseq2.R 17 deseq2.R
11 -o "$deseq_out" 18 -o "$deseq_out"
12 #if $pdf: 19 #if $pdf:
13 -p "$plots" 20 -p "$plots"
33 -b 40 -b
34 #end if 41 #end if
35 #if $many_contrasts: 42 #if $many_contrasts:
36 -m 43 -m
37 #end if 44 #end if
45 ]]>
38 </command> 46 </command>
39 <stdio> 47 <stdio>
40 <regex match="Execution halted" 48 <regex match="Execution halted"
41 source="both" 49 source="both"
42 level="fatal" 50 level="fatal"
117 <output name="deseq_out" file="deseq2_out.tab"/> 125 <output name="deseq_out" file="deseq2_out.tab"/>
118 <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/> 126 <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/>
119 </test> 127 </test>
120 </tests> 128 </tests>
121 <help> 129 <help>
122 130 <![CDATA[
123 .. class:: infomark 131 .. class:: infomark
124 132
125 **What it does** 133 **What it does**
126 134
127 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution 135 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution
165 which controls false discovery rate (FDR) 173 which controls false discovery rate (FDR)
166 ====== ========================================================== 174 ====== ==========================================================
167 175
168 176
169 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html 177 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
170 178 ]]>
171 </help> 179 </help>
172 <citations> 180 <citations>
173 <citation type="doi">10.1186/s13059-014-0550-8</citation> 181 <citation type="doi">10.1186/s13059-014-0550-8</citation>
174 </citations> 182 </citations>
175 </tool> 183 </tool>