--- a/reactome_analysis.py	Tue Mar 05 09:40:41 2019 -0500
+++ b/reactome_analysis.py	Fri Jun 28 05:17:11 2019 -0400
@@ -1,7 +1,4 @@
-import os
-import re
-import json
-import argparse
+import os, re, json, argparse, csv
 
 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
 
@@ -42,22 +39,29 @@
     """
     trash = []
     if identifiers[1] == "list":
-        ids = "\n".join(id_valid(identifiers[0].split())[0])
+        ids = identifiers[0].split()
+        ids = [x.split(";") for x in ids]    
+        ids = [item.strip() for sublist in ids for item in sublist if item != '']
         json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
         if len(id_valid(identifiers[0].split())[1]) > 0:
             trash = id_valid(identifiers[0].split())[1]
     elif identifiers[1] == "file":
         header = identifiers[2]
-        mq = open(identifiers[0]).readlines()
-        if isnumber("int", identifiers[3].replace("c", "")):
-            if header == "true":
-                idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq[1:]]
-            else:
-                idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq]
-            ids = "\n".join(id_valid(idens)[0])
-            json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> stderr" % ids).read()
-            if len(id_valid(idens)[1]) > 0:
-                trash = id_valid(idens)[1]
+        with open(identifiers[0],"r") as mq :
+            file_content = csv.reader(mq,delimiter="\t")
+            file_content = list(file_content)   #csv object to list
+            ncol = identifiers[3]
+            if isnumber("int", ncol.replace("c", "")):
+                if header == "true":
+                    idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]]
+                else:
+                    idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] 
+
+                idens = [item.strip() for sublist in idens for item in sublist if item != '']   #flat list of list of lists, remove empty items 
+                ids = "\n".join(id_valid(idens)[0])
+                json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> stderr" % ids).read()
+                if len(id_valid(idens)[1]) > 0:
+                    trash = id_valid(idens)[1]
     #print(json_string)
     j = json.loads(json_string)
     print ("Identifiers not found: " + str(j["identifiersNotFound"]))

--- a/reactome_analysis.xml	Tue Mar 05 09:40:41 2019 -0500
+++ b/reactome_analysis.xml	Fri Jun 28 05:17:11 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="reactome_analysis" name="Query pathway database" version="2019.03.05">
+<tool id="reactome_analysis" name="Query pathway database" version="2019.06.27">
     <description>[Reactome]</description>
     <requirements>
     </requirements>
@@ -20,7 +20,7 @@
     ]]></command>
     <inputs>
         <conditional name="opt">
-            <param name="input" type="select" label="Input IDs (UniProt Accession number, Entrez Gene ID or Gene Name" multiple="False" >
+            <param name="input" type="select" label="Input IDs (UniProt Accession number, Entrez Gene ID, Gene Name)" multiple="False" >
                 <option value="text">Copy/paste your list of IDs </option>
 		        <option value="file" selected="true">Input file containing your IDs</option>
             </param>
@@ -44,7 +44,7 @@
                 </param>
             </when>
         </conditional>
-        <param name="species" type="select" label="Species">
+        <param name="species" type="select" label="Species (human, mouse, rat)">
             <option value="48887">Human (Homo sapiens)</option>
             <option value="48892">Mouse (Mouse musculus)</option>
             <option value="48895">Rat (Rattus norvegicus)</option>
@@ -82,6 +82,10 @@
 
 ID types allowed are: UniProt accNumber (e.g. O75391), Entrez gene ID (e.g. 8086) and gene name (e.g. TP53, NUP58...). If you have other type of ID, 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.
+
 -----
 
 **Parameters**
@@ -108,13 +112,13 @@
 
 **Galaxy integration**
 
-T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+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>