Mercurial > repos > proteore > proteore_clusterprofiler
changeset 9:2f67202ffdb3 draft
planemo upload commit 6ca074d75447a272b570f7709ed10d0c8356bec5-dirty
| author | proteore |
|---|---|
| date | Wed, 27 Feb 2019 03:39:16 -0500 |
| parents | b29255864039 |
| children | d951677a50d4 |
| files | GO-enrich.R cluster_profiler.xml |
| diffstat | 2 files changed, 12 insertions(+), 5 deletions(-) [+] |
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--- a/GO-enrich.R Fri Dec 21 04:12:32 2018 -0500 +++ b/GO-enrich.R Wed Feb 27 03:39:16 2019 -0500 @@ -156,9 +156,12 @@ #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda") #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda") - plot = unlist(strsplit(args$plot,",")) + go_represent=str2bool(args$go_represent) go_enrich=str2bool(args$go_enrich) + if (go_enrich){ + plot = unlist(strsplit(args$plot,",")) + } suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE))
--- a/cluster_profiler.xml Fri Dec 21 04:12:32 2018 -0500 +++ b/cluster_profiler.xml Wed Feb 27 03:39:16 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.21"> +<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2019.02.18"> <description>(Human, Mouse, Rat)[clusterProfiler]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -32,6 +32,7 @@ #end if #if $ego.go_enrich == "true" + --plot="$ego.plot" --go_enrich="true" --pval_cutoff="$ego.pval" --qval_cutoff="$ego.qval" @@ -51,7 +52,6 @@ --go_enrich="false" #end if - --plot="$ego.plot" --onto_opt="$ontology" > $log ]]></command> <inputs> @@ -75,7 +75,9 @@ <when value="file" > <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> </when> </conditional> <conditional name="idti" > @@ -135,7 +137,9 @@ <when value="file" > <param name="file" type="data" format="txt,tabular" label="Select file that contains your background IDs list" help="" /> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> </when> </conditional> <conditional name="universe_idti" >