Mercurial > repos > proteore > proteore_topgo
diff topGO.xml @ 12:8eaa43ba1bfc draft
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
| author | proteore |
|---|---|
| date | Fri, 28 Jun 2019 05:18:20 -0400 |
| parents | fa2e27165d5d |
| children | aba2aa04c7aa |
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--- a/topGO.xml Mon Mar 04 08:37:49 2019 -0500 +++ b/topGO.xml Fri Jun 28 05:18:20 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="2019.06.27"> <description>(Human, Mouse, Rat)[topGO]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> @@ -51,7 +51,7 @@ <inputs> <conditional name="inputtype"> - <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene only)" help="Copy/paste or from a file"> + <param name="filetype" type="select" label="Enter your IDs (Ensembl Gene Id)" help="Copy/paste or from a file"> <option value="file" selected="true">Input file containing your IDs</option> <option value="copy_paste">Copy/paste your list of IDs</option> </param> @@ -76,7 +76,7 @@ </when> </conditional> <conditional name="background_genes"> - <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Define your own background IDs ?"/> + <param name="background" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Use your own background (ID list) ?"/> <when value="true"> <conditional name="inputtype"> <param name="filetype" type="select" label="Enter your background IDs (Ensembl gene IDs)" help="(e.g : ENSG00000139618)"> @@ -106,7 +106,7 @@ </when> <when value="false"/> </conditional> - <param name="geneuniverse" type="select" label="Species"> + <param name="geneuniverse" type="select" label="Species (human, mouse, rat)"> <!--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--> @@ -120,7 +120,7 @@ <option value="CC" >Cellular Component</option> <option value="MF" >Molecular Function</option> </param> - <param name="option" type="select" label="Select the topGO parameter (see user doc)"> + <param name="option" type="select" label="Select GO scoring method (read user doc section)"> <option value="classic" >Classic Fisher test</option> <option value="elim" selected="true">Elim</option> <option value="weight01" >Weight01</option> @@ -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[ @@ -209,7 +202,7 @@ "GO terms category": select either Biogical Process (BP)(by default), Cellular Component (CC) or Molecular Function (MF) -"Select the topGO parameter (see user doc)": topGO provides a classic Fisher test for evaluating which GO terms are over-represented in your gene/protein list; other methodologies are also provided (Elim, Weight01, Parentchild). For the merits of each option and their algorithmic descriptions, please refer to topGO manual: +"Select GO scoring method: topGO provides the commonly used Fisher test for evaluating which GO terms are over-represented in your gene/protein list; it also provides other GO scoring algorithms (i.e. Elim, Weight01, Parentchild). For the merits of each option and their algorithmic description, please refer to topGO manual: https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf "p-value threshold (e.g : 1e-3)": must be in the form of "1e-5" (i.e. 0.00001) @@ -221,7 +214,7 @@ **Output** -Three outputs are available : a textual output, a barplot and/or a dotplot (set by default) graphical outputs. +Two types of output are available: textual and/or graphical outputs (barplot and/or a dotplot (set by default)). *Textual output* @@ -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. @@ -253,13 +259,13 @@ **Galaxy integration** -Lisa Perus, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Lisa Perus, Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR This work has been partially funded through the French National Agency for Research (ANR) IFB project. -Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. +Help: contact@proteore.org for any questions or concerns about this tool. ]]></help> <citations>