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comparison deseq2.xml @ 8:57e2f9454d9e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 50db5cdaef2ff3e54a63670108eb6e4ade2a630f
author iuc
date Tue, 04 Apr 2017 10:17:29 -0400
parents cb23006f34ff
children 24a09ca67621
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7:cb23006f34ff 8:57e2f9454d9e
1 <tool id="deseq2" name="DESeq2" version="2.11.38"> 1 <tool id="deseq2" name="DESeq2" version="2.11.39">
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 <requirement type="package" version="1.12.4">bioconductor-deseq2</requirement> 4 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <regex match="Execution halted" 7 <regex match="Execution halted"
8 source="both" 8 source="both"
9 level="fatal" 9 level="fatal"
22 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 22 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
23 ]]> 23 ]]>
24 </version_command> 24 </version_command>
25 <command> 25 <command>
26 <![CDATA[ 26 <![CDATA[
27
28 #if $tximport.tximport_selector == 'tximport': 27 #if $tximport.tximport_selector == 'tximport':
29 #if $tximport.mapping_format.mapping_format_selector == 'gtf': 28 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
30 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && 29 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf &&
31 #else: 30 #else:
32 ln -s '$tximport.mapping_format.tabular_file' mapping.txt && 31 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
207 206
208 **What it does** 207 **What it does**
209 208
210 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 209 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
211 210
212
213 **Inputs** 211 **Inputs**
214 212
215 DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level. 213 DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
216 214
217 The following table gives some examples of factors and their levels: 215 The following table gives some examples of factors and their levels:
247 6 p value for the statistical significance of this change 245 6 p value for the statistical significance of this change
248 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure 246 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
249 which controls false discovery rate (FDR) 247 which controls false discovery rate (FDR)
250 ====== ========================================================== 248 ====== ==========================================================
251 249
252
253 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html 250 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
254 ]]> 251 ]]>
255 </help> 252 </help>
256 <citations> 253 <citations>
257 <citation type="doi">10.1186/s13059-014-0550-8</citation> 254 <citation type="doi">10.1186/s13059-014-0550-8</citation>