Mercurial > repos > bgruening > deseq2
changeset 28:6947d8ed51cc draft
Uploaded
| author | bgruening |
|---|---|
| date | Wed, 03 Dec 2014 14:23:27 -0500 |
| parents | 05a4f4e317a0 |
| children | 07620fe97c88 |
| files | deseq2.xml |
| diffstat | 1 files changed, 7 insertions(+), 27 deletions(-) [+] |
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--- a/deseq2.xml Wed Nov 26 12:16:47 2014 -0500 +++ b/deseq2.xml Wed Dec 03 14:23:27 2014 -0500 @@ -24,8 +24,8 @@ #set $temp_factor = list() #for $level in $factor.rep_factorLevel: #set $count_files = list() - #for $file in $level.rep_countsFile: - $count_files.append(str($file.countsFile)) + #for $file in $level.countsFile: + $count_files.append(str($file)) #end for $temp_factor.append( {str($level.factorLevel): $count_files} ) #end for @@ -66,9 +66,7 @@ <valid initial="string.letters,string.digits"><add value="_" /></valid> </sanitizer> </param> - <repeat name="rep_countsFile" title="biological replicate" min="1"> - <param name="countsFile" type="data" label="Counts file"/> - </repeat> + <param name="countsFile" type="data" multiple="true" label="Counts file"/> </repeat> </repeat> <conditional name="filtermode"> @@ -83,7 +81,7 @@ <param name="count_quant" size="10" type="float" value="10.0" min="0" max="100" label="Filter out features with mean normalized counts lower than this % of values" /> </when> </conditional> - <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" label="Visualising the analysis results" + <param name="pdf" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Visualising the analysis results" help="output an additional PDF files" /> </inputs> @@ -101,32 +99,14 @@ <param name="factorName" value="Treatment"/> <repeat name="rep_factorLevel"> <param name="factorLevel" value="Treated"/> - <repeat name="rep_countsFile"> - <param name="countsFile" value="GSM461179_treat_single.counts"/> - </repeat> - <repeat name="rep_countsFile"> - <param name="countsFile" value="GSM461180_treat_paired.counts"/> - </repeat> - <repeat name="rep_countsFile"> - <param name="countsFile" value="GSM461181_treat_paired.counts"/> - </repeat> + <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> </repeat> <repeat name="rep_factorLevel"> <param name="factorLevel" value="Untreated"/> - <repeat name="rep_countsFile"> - <param name="countsFile" value="GSM461176_untreat_single.counts"/> - </repeat> - <repeat name="rep_countsFile"> - <param name="countsFile" value="GSM461177_untreat_paired.counts"/> - </repeat> - <repeat name="rep_countsFile"> - <param name="countsFile" value="GSM461178_untreat_paired.counts"/> - </repeat> - <repeat name="rep_countsFile"> - <param name="countsFile" value="GSM461182_untreat_single.counts"/> - </repeat> + <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> </repeat> </repeat> + <param name="pdf" value="no"/> <output name="deseq_out" file="deseq2_out.tab"/> <output name="deseq_out_filtered" file="deseq2_out_filtered.tab"/> </test>