Mercurial > repos > proteore > proteore_topgo
changeset 6:81d204aac06b draft
planemo upload commit 26575daf6b3f9ed4f203b50e10e58933b94a94c5-dirty
| author | proteore |
|---|---|
| date | Wed, 19 Sep 2018 08:41:49 -0400 |
| parents | fdc8fbfbfcbc |
| children | 8d35400e0325 |
| files | enrichment_v3.R topGO.xml |
| diffstat | 2 files changed, 12 insertions(+), 10 deletions(-) [+] |
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--- a/enrichment_v3.R Fri Sep 14 08:54:43 2018 -0400 +++ b/enrichment_v3.R Wed Sep 19 08:41:49 2018 -0400 @@ -63,7 +63,6 @@ # Parse command line arguments - args = commandArgs(trailingOnly = TRUE) # create a list of the arguments from the command line, separated by a blank space @@ -88,6 +87,9 @@ stop("Not enough/Too many arguments", call. = FALSE) } +#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda") +#load("/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda") + typeinput = options.args[1] listfile = options.args[2] onto = as.character(options.args[3])
--- a/topGO.xml Fri Sep 14 08:54:43 2018 -0400 +++ b/topGO.xml Wed Sep 19 08:41:49 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="topGO" name="topGO" version="2018.09.14"> +<tool id="topGO" name="topGO" version="2018.09.18"> <description> Enrichment analysis for Gene Ontology </description> @@ -10,7 +10,7 @@ <requirement type="package" version="3.5.0">bioconductor-org.ce.eg.db</requirement> <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement> <requirement type="package" version="3.5.0">bioconductor-org.sc.sgd.db</requirement> - <!--requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement--> + <requirement type="package" version="3.5.0">bioconductor-org.at.tair.db</requirement> <requirement type="package" version="1.56.0">bioconductor-graph</requirement> <requirement type="package" version="1.40.0">bioconductor-annotationdbi</requirement> <requirement type="package" version="3.5.0">bioconductor-go.db</requirement> @@ -78,7 +78,7 @@ </when> <when value="file_all"> <param name="genelist" type="data" format="txt,tabular" label="Choose an input file" help="This file must imperatively have 1 column filled with IDs consistent with the database that will be used. Please use the MappingIDs component if this is not the case."/> - <param name="column" type="text" label="Please specify the column where you would like to apply the comparison (e.g : Enter c1)" value="c1"/> + <param name="column" type="text" label="Please specify the column where your Ensembl IDs are (e.g : Enter "c1" for column n°1..)" value="c1"/> <param name="header" type="select" label="Does your file have a header?" multiple="false" optional="false"> <option value="TRUE" selected="true">Yes</option> @@ -87,12 +87,12 @@ </when> </conditional> <param name="geneuniverse" type="select" label="Select a specie"> - <!--option value="org.At.tair.db" >Arabidopsis</option--> - <option value="org.Ce.eg.db" >C.elegans</option> - <option value="org.Dm.eg.db" >Fly</option> - <option value="org.Hs.eg.db" selected="true">Human</option> - <option value="org.Mm.eg.db" >Mouse</option> - <option value="org.Sc.sqd.db" >Yeast</option> + <option value="org.At.tair.db" >Arabidopsis</option> + <option value="org.Ce.eg.db" >Worm (C.elegans)</option> + <option value="org.Dm.eg.db" >Fly (D. melanogaster)</option> + <option value="org.Hs.eg.db" selected="true">Human (H. sapiens)</option> + <option value="org.Mm.eg.db" >Mouse (M. musculus)</option> + <option value="org.Sc.sgd.db" >Yeast (S. cerevisiae)</option> </param> <param name="ontocat" type="select" label="Ontology category">