# HG changeset patch
# User proteore
# Date 1545142944 18000
# Node ID ae9c1f1cdec333a18c022dbb5d7dc2744475d42c
# Parent  def6441d2345239f6d75fb3dc11cd260c5f5ee12
planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba

diff -r def6441d2345 -r ae9c1f1cdec3 kegg_identification.xml
--- a/kegg_identification.xml	Thu Dec 13 04:15:10 2018 -0500
+++ b/kegg_identification.xml	Tue Dec 18 09:22:24 2018 -0500
@@ -22,12 +22,12 @@
     ]]></command>
     <inputs>
         <conditional name="input" >
-            <param name="ids" type="select" label="Enter your list of identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
-                <option value="text">Copy/paste your identifiers</option>
-                <option value="file" selected="true">Input file containing your identifiers</option>
+            <param name="ids" type="select" label="Enter your IDs (Entrez gene IDs, KEGG gene IDs or UniProt Accession number)" 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>
             </param>
             <when value="text" >
-                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' >
+                <param name="txt" type="text" label="Copy/paste your IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: hsa:3306 hsa:22948' >
                     <sanitizer invalid_char=''>
                         <valid initial="string.printable">
                             <remove value="&apos;"/>
@@ -39,23 +39,23 @@
                 </param>
             </when>
             <when value="file" >
-                <param name="file" type="data" format="txt,tabular,tsv" label="Select a file that contains your list of identifiers" help="" />
-                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain a header?" />
-                <param name="ncol" type="text" value="c1" label="The column number of your identifiers to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
+                <param name="file" type="data" format="txt,tabular,tsv" label="Select your file" help="" />
+                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
+                <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
             </when>
         </conditional>
-        <param name="id_type" type="select" label="select your identifiers type :" >
-            <option value="ncbi-geneid" selected="true">Entrez genes ID</option>
-            <option value="kegg-id">KEGG genes ID</option>
-            <option value="uniprot">Uniprot Accession number</option>
+        <param name="id_type" type="select" label="Select IDs" >
+            <option value="ncbi-geneid" selected="true">Entrez Gene ID</option>
+            <option value="kegg-id">KEGG gene ID</option>
+            <option value="uniprot">UniProt Accession number</option>
             
         </param>
-        <param name="species" type="select" label="Select species">
-            <option value="hsa">Human (H. sapiens)</option>
-            <option value="mmu">Mouse (M. musculus)</option>
-            <option value="rno">Rat (R. norvegicus)</option>
+        <param name="species" type="select" label="Species">
+            <option value="hsa">Human (Homo sapiens)</option>
+            <option value="mmu">Mouse (Mus musculus)</option>
+            <option value="rno">Rat (Rattus norvegicus)</option>
         </param>
-        <param type="integer" name="nb_pathways" label="Set the number of pathways to be displayed in the output" value="10" help="Pathways are sorted by percent of mapping gene by pathway in descending order"/>
+        <param type="integer" name="nb_pathways" label="Set number of pathways to be displayed" value="10" help="Pathways are sorted by percent of mapping gene by pathway in descending order"/>
     </inputs>
     <outputs>
         <data name="output1" format="tsv" />
@@ -76,23 +76,34 @@
     </tests>
     <help><![CDATA[
 
-This tool maps a list of identifiers to KEGG pathway and return a list of KEGG pathways ranked by the percentage of coverage for each pathway. This is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes present in the considered species for each KEGG pathway. 
+**Description**
 
-It allows you to directly identify the signaling pathways that are the most covered by your proteomics dataset. 
+This tool maps a list of identifiers to all KEGG pathways and returns a list of KEGG pathways sorted by the percentage of coverage for each pathway. This is done by computing the number of KEGG genes IDs from your list divided by the total number of KEGG genes ID of the selected species for each KEGG pathway. 
 
-By default the number of pathway to be displayed is set to 10 and sorted in descending order. 
+It allows you to directly identify KEGG pathways that are the most covered by your gene/protein list. 
 
-At the moment three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus).
+-----
 
-**Input:**
+**Input**
 
-Input can be either a list of ids or a file containing multiple columns but with at least one column of ids (e.g. hsa04970). 
-Input ids type can be Entrez gene ID, KEGG gene ID or Uniprot accession number.
+Input can be either a list of IDs or a file containing multiple columns but with at least one column of IDs (e.g. hsa:04970). 
+Input IDs type can be Entrez gene ID (e.g. 2243), KEGG gene ID (e.g. hsa:2243 in homo sapiens) or Uniprot accession number (e.g. P02671).
 
 .. class:: warningmark  
 
-If you use Uniprot accession number, it will be converted to KEGG gene ID, this step can be time consuming.
-If your input file contains other type of ids, please use the ID_Converter tool.
+If you use Uniprot accession number, it will be converted to KEGG gene ID; this step can be time consuming.
+
+If your input file contains other type of ID, please use the ID_Converter tool.
+
+-----
+
+**Parameters**
+
+"Set number of pathways to be displayed": by default the number of pathway to be displayed is set to 10 and sorted in descending order. 
+
+"Species": three species are supported: Human (Homo sapiens), Mouse (Mus musculus) and Rat (Rattus norvegicus).
+
+-----
 
 **Output:**
 
@@ -100,21 +111,20 @@
 
 * **Pathway_ID:** KEGG pathway identifier (e.g. hsa04970)
 * **Description:** name of the pathway as in KEGG
-* **Ratio IDs mapped/total IDs (%):** percentage of pathway coverage
-* **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes of your list mapped on the KEGG pathway
-* **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway
+* **Ratio IDs mapped/total IDs (%):** pathway coverage in percentage
+* **nb KEGG genes IDs mapped in the pathway:** number of KEGG genes from your list mapped to the KEGG pathway
+* **nb total of KEGG genes IDs present in the pathway:** total number of KEGG genes present in the KEGG pathway 
 
 -----
 
 .. class:: infomark
 
-**Database:**
+**Data source (release date)**
 
 Pathways and KEGG genes IDs are collected via KEGGREST package. 
 
 User manual / Documentation: KEGGREST Bioconductor package https://bioconductor.org/packages/3.1/bioc/html/KEGGREST.html
 
-
 -----
 
 .. class:: infomark
@@ -123,7 +133,7 @@
 
 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
-Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
+Sandra Dérozier, Olivier Rué, 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.