Mercurial > repos > proteore > proteore_topgo
diff topGO.xml @ 20:537a0aae9b41 draft
planemo upload commit 065ae340a41e0cf514fe067cb72b6994327163f3-dirty
| author | proteore |
|---|---|
| date | Mon, 03 Jun 2019 11:35:10 -0400 |
| parents | 0014bd289aff |
| children | 79d0f1773124 |
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--- a/topGO.xml Tue Feb 19 08:47:25 2019 -0500 +++ b/topGO.xml Mon Jun 03 11:35:10 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.02.19"> +<tool id="topGO" name="Enrichment analysis for Gene Ontology" version="2019.06.01"> <description>(Human, Mouse, Rat)[topGO]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -170,19 +170,12 @@ <param name="option" value="elim"/> <param name="threshold" value="1e-3"/> <param name="correction" value="BH"/> - <conditional name="condtext"> - <param name="textoutput" value="TRUE"/> - </conditional> - <conditional name="condbar"> - <param name="barplotoutput" value="TRUE"/> - </conditional> - <conditional name="conddot"> - <param name="dotoutput" value="TRUE"/> - </conditional> + <param name="textoutput" value="TRUE"/> + <param name="plot" value="dotplot,barplot"/> <param name="geneuniverse" value="org.Hs.eg.db"/> - <output name="outputtext" file="Text_output_for_topGO_analysis_BP_category.tabular"/> - <output name="outputbarplot" file="Barplot_output_for_topGO_analysis_BP_category.png"/> - <output name="outputdotplot" file="Dotplot_output_for_topGO_analysis_BP_category.png"/> + <output name="outputtext" file="result.tsv"/> + <output name="outputbarplot" file="barplot.png" compare="sim_size"/> + <output name="outputdotplot" file="dotplot.png" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -243,6 +236,19 @@ .. class:: infomark +Packages used: + - bioconductor-org.hs.eg.db v3.5.0 + - bioconductor-org.mm.eg.db v3.5.0 + - bioconductor-org.rn.eg.db v3.5.0 + - bioconductor-annotationdbi v1.40.0 + - bioconductor-go.db v3.5.0 + - bioconductor-graph v1.56.0 + - bioconductor-topgo v2.30.0 + +----- + +.. class:: infomark + **Authors** Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006. 22(13):1600-7. PubMed PMID: 16606683.