| Previous changeset 1:6788a57c5cb5 (2018-02-16) Next changeset 3:5f6d95716bc9 (2018-02-27) |
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Commit message:
planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty |
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modified:
README.rst topGO.xml |
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| diff -r 6788a57c5cb5 -r f62d29616966 README.rst --- a/README.rst Fri Feb 16 04:15:08 2018 -0500 +++ b/README.rst Tue Feb 27 09:09:42 2018 -0500 |
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| @@ -1,5 +1,5 @@ Wrapper for topGO -============================= +================= **Authors** @@ -15,7 +15,7 @@ Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. -============================= +=================== **Galaxy component based on R package topGO.** |
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| diff -r 6788a57c5cb5 -r f62d29616966 topGO.xml --- a/topGO.xml Fri Feb 16 04:15:08 2018 -0500 +++ b/topGO.xml Tue Feb 27 09:09:42 2018 -0500 |
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| @@ -3,6 +3,8 @@ performs enrichment analysis using R package topGO </description> <requirements> + <requirement type="package" version="3.4.1">R</requirement> + <requirement type="package" version="2.2.1">r-ggplot2</requirement> <requirement type="package" version="1.54.0">bioconductor-graph</requirement> <requirement type="package" version="2.28.0">bioconductor-topgo</requirement> </requirements> @@ -12,13 +14,36 @@ <command><![CDATA[ #if $inputtype.filetype == "file_all": - Rscript --vanilla $__tool_directory__/enrichment_v3.R --inputtype tabfile --input '$inputtype.genelist' --ontology '$ontocat' --option '$option' --threshold '$threshold' --correction '$correction' --textoutput '$condtext.textoutput' --barplotoutput '$condbar.barplotoutput' --dotplotoutput '$conddot.dotplotoutput' --column '$inputtype.column' --geneuniverse '$geneuniverse' --header '$inputtype.header' + Rscript --vanilla $__tool_directory__/enrichment_v3.R + --inputtype tabfile + --input '$inputtype.genelist' + --ontology '$ontocat' + --option '$option' + --threshold '$threshold' + --correction '$correction' + --textoutput '$condtext.textoutput' + --barplotoutput '$condbar.barplotoutput' + --dotplotoutput '$conddot.dotplotoutput' + --column '$inputtype.column' + --geneuniverse '$geneuniverse' + --header '$inputtype.header' #end if - #if $inputtype.filetype == "copy_paste": - Rscript --vanilla $__tool_directory__/enrichment_v3.R --inputtype copypaste --input '$inputtype.genelist' --ontology '$ontocat' --option '$option' --threshold '$threshold' --correction '$correction' --textoutput '$condtext.textoutput' --barplotoutput '$condbar.barplotoutput' --dotplotoutput '$conddot.dotplotoutput' --column c1 --geneuniverse '$geneuniverse' --header None - + #if $inputtype.filetype == "copy_paste": + Rscript --vanilla $__tool_directory__/enrichment_v3.R + --inputtype copypaste + --input '$inputtype.genelist' + --ontology '$ontocat' + --option '$option' + --threshold '$threshold' + --correction '$correction' + --textoutput '$condtext.textoutput' + --barplotoutput '$condbar.barplotoutput' + --dotplotoutput '$conddot.dotplotoutput' + --column c1 + --geneuniverse '$geneuniverse' + --header None #end if |