Mercurial > repos > proteore > proteore_topgo
comparison topGO.xml @ 2:f62d29616966 draft
planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
| author | proteore |
|---|---|
| date | Tue, 27 Feb 2018 09:09:42 -0500 |
| parents | 6788a57c5cb5 |
| children | 5f6d95716bc9 |
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| 1:6788a57c5cb5 | 2:f62d29616966 |
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| 1 <tool id="topGO" name="topGO enrichment analysis" version="0.1.0"> | 1 <tool id="topGO" name="topGO enrichment analysis" version="0.1.0"> |
| 2 <description> | 2 <description> |
| 3 performs enrichment analysis using R package topGO | 3 performs enrichment analysis using R package topGO |
| 4 </description> | 4 </description> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="3.4.1">R</requirement> | |
| 7 <requirement type="package" version="2.2.1">r-ggplot2</requirement> | |
| 6 <requirement type="package" version="1.54.0">bioconductor-graph</requirement> | 8 <requirement type="package" version="1.54.0">bioconductor-graph</requirement> |
| 7 <requirement type="package" version="2.28.0">bioconductor-topgo</requirement> | 9 <requirement type="package" version="2.28.0">bioconductor-topgo</requirement> |
| 8 </requirements> | 10 </requirements> |
| 9 <stdio> | 11 <stdio> |
| 10 <exit_code range="1:" /> | 12 <exit_code range="1:" /> |
| 11 </stdio> | 13 </stdio> |
| 12 <command><![CDATA[ | 14 <command><![CDATA[ |
| 13 | 15 |
| 14 #if $inputtype.filetype == "file_all": | 16 #if $inputtype.filetype == "file_all": |
| 15 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' | 17 Rscript --vanilla $__tool_directory__/enrichment_v3.R |
| 18 --inputtype tabfile | |
| 19 --input '$inputtype.genelist' | |
| 20 --ontology '$ontocat' | |
| 21 --option '$option' | |
| 22 --threshold '$threshold' | |
| 23 --correction '$correction' | |
| 24 --textoutput '$condtext.textoutput' | |
| 25 --barplotoutput '$condbar.barplotoutput' | |
| 26 --dotplotoutput '$conddot.dotplotoutput' | |
| 27 --column '$inputtype.column' | |
| 28 --geneuniverse '$geneuniverse' | |
| 29 --header '$inputtype.header' | |
| 16 #end if | 30 #end if |
| 17 | 31 |
| 18 | 32 |
| 19 #if $inputtype.filetype == "copy_paste": | 33 #if $inputtype.filetype == "copy_paste": |
| 20 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 | 34 Rscript --vanilla $__tool_directory__/enrichment_v3.R |
| 21 | 35 --inputtype copypaste |
| 36 --input '$inputtype.genelist' | |
| 37 --ontology '$ontocat' | |
| 38 --option '$option' | |
| 39 --threshold '$threshold' | |
| 40 --correction '$correction' | |
| 41 --textoutput '$condtext.textoutput' | |
| 42 --barplotoutput '$condbar.barplotoutput' | |
| 43 --dotplotoutput '$conddot.dotplotoutput' | |
| 44 --column c1 | |
| 45 --geneuniverse '$geneuniverse' | |
| 46 --header None | |
| 22 #end if | 47 #end if |
| 23 | 48 |
| 24 | 49 |
| 25 | 50 |
| 26 ]]></command> | 51 ]]></command> |