# HG changeset patch
# User proteore
# Date 1561713075 14400
# Node ID 3ddc1f78773d431ab96a2a07cde882b9f5f9a6e4
# Parent  2138e0035e57f68ae44aaeda3feffc948d0b5e72
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty

diff -r 2138e0035e57 -r 3ddc1f78773d README.rst
--- a/README.rst	Mon Mar 04 08:20:52 2019 -0500
+++ b/README.rst	Fri Jun 28 05:11:15 2019 -0400
@@ -28,3 +28,11 @@
 For more details about GoProfiles, please read: Salicrú et al. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011;12:401.(https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-401)  
 
 If your type of identifiers is not supported (i.e. different form Uniprot and Entrez), please use the **ID Converter** component in the ProteoRE section to convert your list of IDs first.
+
+
+**Packages used**
+    - bioconductor-org.hs.eg.db v3.5.0
+    - bioconductor-org.mm.eg.db v3.5.0
+    - bioconductor-annotationdbi v1.40.0
+    - bioconductor-biobase v2.98.0
+    - goprofiles v1.38.0
diff -r 2138e0035e57 -r 3ddc1f78773d goprofiles.R
--- a/goprofiles.R	Mon Mar 04 08:20:52 2019 -0500
+++ b/goprofiles.R	Fri Jun 28 05:11:15 2019 -0400
@@ -65,20 +65,13 @@
   # Extract Gene Entrez ID
   if (id_type == "Entrez") {
     id = select(package, ids, "ENTREZID", multiVals = "first")
-    genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
   } else {
-    genes_ids = c()
     id = select(package, ids, "ENTREZID", "UNIPROT", multiVals = "first")
-    if (duplicate == "TRUE") {
-      id = unique(id)
-    }
-    print(id[[1]])
-    genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
-    # IDs that have NA ENTREZID
-    NAs = id$UNIPROT[which(is.na(id$ENTREZID))]
-    #print("IDs unable to convert to ENTREZID: ")
-    #print(NAs)
   }
+  if (duplicate) { id = unique(id) }
+  genes_ids = id$ENTREZID[which( ! is.na(id$ENTREZID))]
+  NAs = id$UNIPROT[which(is.na(id$ENTREZID))] # IDs that have NA ENTREZID
+  
   # Create basic profiles
   profile.CC = basicProfile(genes_ids, onto='CC', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
   profile.BP = basicProfile(genes_ids, onto='BP', level=level, orgPackage=species, empty.cats=F, ord=T, na.rm=T)
@@ -163,7 +156,7 @@
   id_type = args$id_type
   input_type = args$input_type
   if (input_type == "text") {
-    input = strsplit(args$input, "[ \t\n]+")[[1]]
+    input = unlist(strsplit(strsplit(args$input, "[ \t\n]+")[[1]],";"))
   } else if (input_type == "file") {
     filename = args$input
     ncol = args$ncol
@@ -178,8 +171,8 @@
     file = read_file(filename, header)
     # Extract Protein IDs list
     input = unlist(strsplit(as.character(file[,ncol]),";"))
-    input = input [which(!is.na(input))]
   }
+  input = input [which(!is.na(gsub("NA",NA,input)))]
   
   if (! any(check_ids(input,id_type))){
     stop(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file"))
@@ -191,7 +184,7 @@
   level = args$level
   per = as.logical(args$per)
   title = args$title
-  duplicate = args$duplicate
+  duplicate = str2bool(args$duplicate)
   text_output = args$text_output
   species=args$species
 
diff -r 2138e0035e57 -r 3ddc1f78773d goprofiles.xml
--- a/goprofiles.xml	Mon Mar 04 08:20:52 2019 -0500
+++ b/goprofiles.xml	Fri Jun 28 05:11:15 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.02.27.1">
+<tool id="goProfiles" name="Statistical analysis of functional profiles" version="2019.06.27">
     <description>(Human, Mouse) [goProfiles]</description>
     <requirements> 
         <requirement type="package" version="3.4.1">R</requirement>
@@ -70,7 +70,7 @@
                 </param>
             </when>            
         </conditional>
-        <param name="duplicate" type="boolean" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
+        <param name="duplicate" type="boolean" checked="true" label="Remove duplicated IDs" truevalue="TRUE" falsevalue="FALSE" />
         <param name="species" type="select" label="Species">
             <option value="org.Hs.eg.db">Human (Homo sapiens)</option>
             <option value="org.Mm.eg.db">Mouse (Mus musculus)</option>
@@ -146,7 +146,7 @@
 
 **Description**
 
-This tool is based on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
+This tool relies on the goProfiles R package; it performs statistical analysis of functional profiles based on Gene Ontology (GO). Functional profile at a given GO level is obtained by counting the
 number of identifiers having a hit in each category of this level.   
 
 -----
@@ -154,7 +154,11 @@
 **Input** 
 
 Two modes are allowed: either by copy/pasting your IDs (separated by a space) or by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers).
-Only entrez gene ID (e.g : 4151) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE. 
+Only entrez gene ID (e.g. 4151) or Uniprot accession number (e.g. P31946) are allowed. If your list is not in this form, please use the ID_Converter tool of ProteoRE. 
+
+.. class:: warningmark
+	
+In copy/paste mode, the number of IDs considered in input is limited to 5000.
 
 -----
 
@@ -172,7 +176,18 @@
 
 Diagram output: graphical output in the form of bar-plot or dot-plot (png (default format), jpeg or pdf format), one figure for each GO category. 
 
-text output: 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)
+Text output: 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)
+
+-----
+
+.. class:: infomark
+
+Packages used: 
+    - bioconductor-org.hs.eg.db v3.5.0
+    - bioconductor-org.mm.eg.db v3.5.0
+    - bioconductor-annotationdbi v1.40.0
+    - bioconductor-biobase v2.98.0
+    - goprofiles v1.38.0
 
 -----
 
@@ -188,14 +203,13 @@
 
 **Galaxy integration**
 
-T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+D. Christiany, T.P. 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>
     </citations>