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changeset 5:8a91f58782df draft

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planemo upload commit c5f2b4b085a9911d1e4cc8d11367dd0363e626ab-dirty
author proteore
date Fri, 23 Mar 2018 10:01:41 -0400
parents 710414ebb6db
children 5e16cec55146
files GO-enrich.R cluster_profiler.xml
diffstat 2 files changed, 33 insertions(+), 45 deletions(-) [+]
line wrap: on
line diff
--- a/GO-enrich.R	Tue Mar 20 08:59:51 2018 -0400
+++ b/GO-enrich.R	Fri Mar 23 10:01:41 2018 -0400
@@ -32,7 +32,7 @@
                readable=TRUE)
   name <- paste("GGO.", ontology, ".png", sep = "")
   png(name)
-  p <- barplot(ggo)
+  p <- barplot(ggo, showCategory=10)
   print(p)
   dev.off()
   return(ggo)
@@ -55,7 +55,7 @@
   dev.off()
   dot_name <- paste("EGO.", ontology, ".dot.png", sep = "")
   png(dot_name)
-  p <- dotplot(ego)
+  p <- dotplot(ego, showCategory=10)
   print(p)
   dev.off()
   return(ego)
--- a/cluster_profiler.xml	Tue Mar 20 08:59:51 2018 -0400
+++ b/cluster_profiler.xml	Fri Mar 23 10:01:41 2018 -0400
@@ -48,7 +48,7 @@
         <conditional name="input" >
             <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
                 <option value="text">Copy/paste your identifiers</option>
-                <option value="file">Input file containing your identifiers</option>
+                <option value="file" selected="true">Input file containing your identifiers</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: P31946 P62258' >
@@ -100,23 +100,6 @@
             </when>
             <when value="false"/>
         </conditional>
-        <!--conditional name="fun" >
-		    <param name="go_function" type="select" display="checkboxes" multiple="true" label="Please select analyses to perform">
-			    <option value="ggo">GO categories representation</option>
-			    <option value="ego">GO categories enrichment (compared to a background/reference)</option>
-		    </param>			
-        	<when value="ggo" >
-			<param name="level" type="select" label="Level of the ontology at which the profile has to be built (the higher this number, the deeper the GO level)">
-				<option value="1">1</option>
-				<option value="2">2</option>
-				<option value="3" selected="True">3</option>
-			</param>
-		    </when>
-		    <when value="ego" >
-			    <param name="pval" type="float" value="0.01" label="P-value cut off"/>
-			    <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
-		    </when>
-	    </conditional-->
 				
 		<param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
             <option value="CC">Cellular Component</option>
@@ -161,45 +144,50 @@
     </tests>
     <help><![CDATA[
        
- 	**Galaxy component based on R package clusterProfiler (see ref below)**
+**Galaxy component based on R package clusterProfiler (see ref below)**
  	
-	This component allows to perform GO enrichment-analyses. 
-	Given a list of IDs, the tool either 
-	(i)  performs gene classification based on GO distribution at a specific level, or
-	(ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, 
-	compared to a background (whole organism or user-defined list). 
+This component allows to perform GO enrichment-analyses.
+
+Given a list of IDs, the tool either 
+  (i)  performs gene classification based on GO distribution at a specific level, or
+  (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background (whole organism or user-defined list). 
 
-	**Input required**
+**Input required**
 
-	This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). 
-	You can copy/paste these identifiers or supply a tabular file (.csv, .tsv, .txt, .tab) where there are contained.
+This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). 
+
+Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) 
+or by copy/pasting your IDs (separated by a space).
 
  
-	**Output**
+**Output**
 
-	Text (tables) and graphics representing the repartition and/or enrichment of GO categories. 
+Text (tables) and graphics representing the repartition and/or enrichment of GO categories. 
 
-	**User manual / Documentation** of the clusterProfiler R package (functions and parameters):
-	https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
-	(Very well explained)
+**User manual / Documentation** of the clusterProfiler R package (functions and parameters):
+https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
+(Very well explained)
 
-	**Reference**
+**Reference**
  
-	clusterProfiler R package reference : 
-	G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. 
-	OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. 
-	doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
+clusterProfiler R package reference : 
+G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. 
+OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. 
+doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
 
-	
-	**Galaxy integration**
+-----
+
+.. class:: infomark
 
-	T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+**Galaxy integration**
 
-	Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
-	This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
 
-	Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+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>