Mercurial > repos > proteore > proteore_go_terms_enrich_comparison
changeset 6:f53249651add draft
planemo upload commit c9d70181a2b587e53dcc4b5885b74b625def6b8c-dirty
| author | proteore |
|---|---|
| date | Thu, 23 Jan 2020 03:16:11 -0500 |
| parents | a6e33a8ae6ff |
| children | 2e7245bd643d |
| files | GO_terms_enrich_comparison.xml |
| diffstat | 1 files changed, 13 insertions(+), 15 deletions(-) [+] |
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--- a/GO_terms_enrich_comparison.xml Tue Jan 14 08:51:51 2020 -0500 +++ b/GO_terms_enrich_comparison.xml Thu Jan 23 03:16:11 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2020.01.14"> +<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2020.01.23"> <description>(Human, Mouse, Rat)[clusterProfiler]</description> <requirements> <requirement type="package">R</requirement> @@ -38,9 +38,9 @@ <repeat name="lists" title="List to compare" min="2" max="5" > <conditional name="input" > - <param name="ids" type="select" label="Enter your Gene ID list" help="Copy/paste or from a file (e.g. table)" > + <param name="ids" type="select" label="Enter your ID list (Entrez gene ID, e.g. 2810)" help="Copy/paste or from a file (e.g. table)" > <option value="text">Copy/paste your IDs</option> - <option value="file" selected="true">Input file containing your IDs</option> + <option value="file" selected="true">Input file containing your list of IDs</option> </param> <when value="text" > <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: 2810 7534' > @@ -63,7 +63,7 @@ </when> </conditional> - <param name="list_name" type="text" label="name of your list" value="list" optional="false"> + <param name="list_name" type="text" label="name of your list" value="List" optional="false"> <sanitizer> <valid initial="string.printable"> <remove value="'"/> @@ -135,11 +135,9 @@ **Description** -This tool is based on the R package clusterProfiler and allows to compare GO terms enrichment analyses of gene/protein sets. +This tool is based on the R package clusterProfiler and was developed for biological theme comparison; it provides a function to automatically calculate enriched functional categories of each gene clusters provided by the user and to compare them. Given a list of gene set, this function will compute GO enrichment profiles of each gene list. -This tool calculates GO categories enrichment (over- or under-representation) for the IDs of the input list. - ----- **Input** @@ -149,17 +147,17 @@ "Enter your Gene ID list": only Entrez Gene ID (e.g : 4151, 7412). If your IDs are not Entrez Gene IDs, please use the ID_Converter tool of ProteoRE. -"Does file contain header?": in case of file input, you specify if there is header or not. +"Does file contain header?": specify if there is header in your input file. -"Column number of IDs": in which column are your IDs. (e.g. for column 2 you write "c2") +"Column number of IDs": in which column are your IDs. (e.g. for column 2, type "c2") -"name of your list": write the name for this list +"name of your list": enter a name for each list ("List" by default); this name will be used in the output files. up to five lists can be considered ----- **Parameters** -"Species": the three supported species are Homo sapiens, Mus musculus and Rattus norvegicus +"Species": the following three species are currently supported: Homo sapiens, Mus musculus and Rattus norvegicus "Select GO terms category": allows you to perform analysis on one, two or three categories of the Gene Ontology. The categories are Cellular Component (CC), Biological Process (BP) and Molecular Function (MF). @@ -168,10 +166,10 @@ **Output** -Diagram output: graphical output in the form of a dot-plot (png, jpeg or pdf format), one figure for each GO category. -Text tables: with the following information GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) +Diagram output: graphical output in the form of a dot-plot (png, jpeg or pdf format), one figure for each GO category. The dots size correspond to the value of the GeneRatio (i.e. gene counts / total number of gene list), the bigger the dot size, the higher the GeneRatio. The dots in the plot are color-coded based on their corresponding (adjusted) p-values. Color gradient ranging from red to blue correspond to in order of increasing p-values. That is, red indicate low p-values (high enrichment), and blue indicate high p-values (low enrichment). +Text tables with the following information: GO category description (e.g.BP.Description), GO term identifier (e.g. BP.GOID) and GO term frequency (e.g. BP.Frequency). -One table and one graphic will be produced for each GO category. +One table and one graphic are created for each GO category. ----- @@ -190,7 +188,7 @@ 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 +David Christiany, 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.