# HG changeset patch
# User proteore
# Date 1544197437 18000
# Node ID 8200968789c179785e15a31454d7b78d11454025
# Parent  19d8daa1eb2ef11df23f5b12434baf526afbad05
planemo upload commit 1b95e5bc85662f10cdd6305587ccee8faf9a2354-dirty

diff -r 19d8daa1eb2e -r 8200968789c1 reactome_analysis.py
--- a/reactome_analysis.py	Mon Nov 26 04:48:25 2018 -0500
+++ b/reactome_analysis.py	Fri Dec 07 10:43:57 2018 -0500
@@ -45,7 +45,7 @@
         ids = "\n".join(id_valid(identifiers[0].split())[0])
         #print(ids)
         #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
-        json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read()
+        json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
         if len(id_valid(identifiers[0].split())[1]) > 0:
             trash = id_valid(identifiers[0].split())[1]
     elif identifiers[1] == "file":
@@ -59,13 +59,13 @@
             ids = "\n".join(id_valid(idens)[0])
             #print(ids)
             #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
-            json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read()
+            json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
             if len(id_valid(idens)[1]) > 0:
                 trash = id_valid(idens)[1]
     print(json_string)
     return json_string, trash
 
-def write_output(filename, json_string, trash_file, trash):
+def write_output(filename, json_string, species, trash_file, trash):
     """
     Replace json result in template and print to output
     """
@@ -74,6 +74,7 @@
     try: 
         for line in template:
             if "{token}" in line:
+                line = line.replace("{species}", species)
                 line = line.replace("{token}", json.loads(json_string)["summary"]["token"])
             output.write(line)
     except ValueError:
@@ -92,10 +93,11 @@
     argument = parser.add_argument("--json", nargs="+", required=True)
     argument = parser.add_argument("--output", default="output.html")
     argument = parser.add_argument("--trash", default="trash.txt")
+    argument = parser.add_argument("--species", default="48887")
     args = parser.parse_args()
     filename = args.output
     json_string, trash = data_json(args.json)
-    write_output(filename, json_string, args.trash, trash)
+    write_output(filename, json_string, args.species, args.trash, trash)
 
 if __name__ == "__main__":
     options()
diff -r 19d8daa1eb2e -r 8200968789c1 reactome_analysis.xml
--- a/reactome_analysis.xml	Mon Nov 26 04:48:25 2018 -0500
+++ b/reactome_analysis.xml	Fri Dec 07 10:43:57 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="reactome_analysis" name="Reactome" version="2018.10.12">
+<tool id="reactome_analysis" name="Reactome" version="2018.12.07">
     <description>display your protein list on the Reactome pathway browser</description>
     <requirements>
     </requirements>
@@ -6,11 +6,16 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
+
+        python $__tool_directory__/reactome_analysis.py 
         #if $opt.input == "text"
-            python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash"
+        --json "$opt.list" "list" 
         #else if $opt.input == "file"
-            python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash"
+        --json "$opt.file" "file" "$opt.header" "$opt.ncol" 
         #end if
+        --output "$output" 
+        --trash "$trash"
+        --species "$species"
         
     ]]></command>
     <inputs>
@@ -36,8 +41,12 @@
                 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
 		        <param type="text" name="ncol" value="c1" label="Please specify the column number where are your IDs (e.g : Enter c1 for column n°1)" />
             </when>
-            
         </conditional>
+        <param name="species" type="select" label="Select species">
+            <option value="48887">Human (H. sapiens)</option>
+            <option value="48892">Mouse (M. musculus)</option>
+            <option value="48895">Rat (R. norvegicus)</option>
+        </param>
     </inputs>
     <outputs>
         <data name="output" format="html" label="" />
@@ -64,6 +73,8 @@
 
 **Supported IDs: Uniprot accession number (e.g. P01023), Entrez gene ID (e.g.7157), gene name (e.g. AQP7). If there is any ID containing invalid characters, it will be removed from the queue and placed in "Invalid identifiers" file.**
 
+**Supported species: Human (H. sapiens), Mouse (M. musculus), Rat (Rattus norvegicus)**
+
 -----
 
 .. class:: infomark
diff -r 19d8daa1eb2e -r 8200968789c1 template.html
--- a/template.html	Mon Nov 26 04:48:25 2018 -0500
+++ b/template.html	Fri Dec 07 10:43:57 2018 -0500
@@ -35,7 +35,7 @@
 
     <p>Please click the button to execute the analysis:</p>
 
-    <form action="http://www.reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS={token}" target="_blank">
+    <form action="http://www.reactome.org/PathwayBrowser/#/SPECIES={species}&DTAB=AN&ANALYSIS={token}" target="_blank">
     
     <button>Analyse</button>