Mercurial > repos > iuc > deseq2
diff deseq2.xml @ 6:982bd8bfa44c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 470804fe1d65ce5bf49804c7f249c51f6a567f9f
| author | iuc |
|---|---|
| date | Sat, 05 Sep 2015 04:37:45 -0400 |
| parents | 4ba2afa87fce |
| children | 681fd2c5f47a |
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--- a/deseq2.xml Fri Sep 04 08:26:02 2015 -0400 +++ b/deseq2.xml Sat Sep 05 04:37:45 2015 -0400 @@ -6,16 +6,29 @@ <requirement type="package" version="3.10.2">atlas</requirement> <requirement type="package" version="1.8.1">deseq2</requirement> </requirements> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> <version_command> <![CDATA[ - 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: ") + echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]> </version_command> <command interpreter="Rscript"> <![CDATA[ #import json - \$DESEQ2_ROOT_PATH/inst/script/deseq2.R + \$DESEQ2_ROOT_PATH/script/deseq2.R -o "$deseq_out" #if $pdf: -p "$plots" @@ -45,16 +58,6 @@ #end if ]]> </command> - <stdio> - <regex match="Execution halted" - source="both" - level="fatal" - description="Execution halted." /> - <regex match="Error in" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - </stdio> <inputs> <repeat name="rep_factorName" title="Factor" min="1"> <param name="factorName" type="text" value="FactorName" label="Specify a factor name" @@ -70,7 +73,7 @@ <valid initial="string.letters,string.digits"><add value="_" /></valid> </sanitizer> </param> - <param name="countsFile" type="data" multiple="true" label="Counts file(s)"/> + <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> </repeat> </repeat> <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"