# HG changeset patch
# User proteore
# Date 1536330081 14400
# Node ID 39d3478fbc5e089064376f607c897034a9495862
# Parent  1704d57a04ba337e019e18250d4efc5d3a5340f6
planemo upload commit eed8cd910cd0eb3992d2188485b6ac5fdbc55eea

diff -r 1704d57a04ba -r 39d3478fbc5e compute_kegg_pathways.xml
--- a/compute_kegg_pathways.xml	Thu Sep 06 08:41:40 2018 -0400
+++ b/compute_kegg_pathways.xml	Fri Sep 07 10:21:21 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="compute_kegg_pathways" name="Compute KEGG pathways coverage using KEGG REST api" version="2018.09.06">
+<tool id="compute_kegg_pathways" name="Compute KEGG pathways coverage using KEGG REST api" version="2018.09.07">
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
     </requirements>
@@ -16,12 +16,12 @@
         --id_type="$ref_ids.id_type"
         --output="$output1" 
         --nb_pathways="$nb_pathways"
-        --ref="$ref_ids.ref_file"
+        --ref="$__tool_directory__/$ref_ids.ref_file"
 
     ]]></command>
     <inputs>
         <conditional name="input" >
-            <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" >
+            <param name="ids" type="select" label="Provide your identifiers (Uniprot or Entrez gene)" 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>
@@ -51,19 +51,19 @@
             <when value="uniprot">
                 <param name="ref_file" type="select" label="Select species" >
                     <options from_data_table="uniprot_kegg_list"/>
-                        <option>Human</option>
-                        <option>Mouse</option>
+                        <option>Human (Homo sapiens)</option>
+                        <option>Mouse (Mus musculus)</option>
                 </param>
             </when>
             <when value="geneID">
                 <param name="ref_file" type="select" label="Select species" >
                     <options from_data_table="entrez_kegg_list"/>
-                        <option>Human</option>
-                        <option>Mouse</option>
+                        <option>Human (Homo sapiens)</option>
+                        <option>Mouse (Mus musculus)</option>
                 </param>
             </when>
         </conditional>
-        <param type="integer" name="nb_pathways" label="Set the number of pathways to keep in result" value="10" help="pathways are sorted by percent of mapping gene by pathway in descending order"/>
+        <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"/>
     </inputs>
     <outputs>
         <data name="output1" format="tsv" />
@@ -76,7 +76,7 @@
 
 By default the number of pathway to be displayed is set to 10 and sorted in descending order. 
 
-At the moment two species are considered: Human (Homo sapiens) and Mouse (Mus musculus)
+At the moment two species are supported: Human (Homo sapiens) and Mouse (Mus musculus)
 
 **Input:**
 
@@ -150,4 +150,4 @@
   url = {https://github.com/Bioconductor/KEGGREST},
 }</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r 1704d57a04ba -r 39d3478fbc5e entrez_kegg_list.loc.sample
--- a/entrez_kegg_list.loc.sample	Thu Sep 06 08:41:40 2018 -0400
+++ b/entrez_kegg_list.loc.sample	Fri Sep 07 10:21:21 2018 -0400
@@ -1,3 +1,3 @@
 #name	date	organism	value(path)
-Human	27-07-18	hsa	tool_data/l.hsa.gene.RData
-Mouse	27-07-18	mmu	tool_data/l.mmu.gene.RData
+Human	27-07-18	hsa	tool-data/l.hsa.gene.RData
+Mouse	27-07-18	mmu	tool-data/l.mmu.gene.RData
diff -r 1704d57a04ba -r 39d3478fbc5e uniprot_kegg_list.loc.sample
--- a/uniprot_kegg_list.loc.sample	Thu Sep 06 08:41:40 2018 -0400
+++ b/uniprot_kegg_list.loc.sample	Fri Sep 07 10:21:21 2018 -0400
@@ -1,3 +1,3 @@
 #name	date	organism	value(path)
-Human	27-07-18	hsa	tool_data/l.hsa.up.RData
-Mouse	27-07-18	mmu	tool_data/l.mmu.up.RData
+Human	27-07-18	hsa	tool-data/l.hsa.up.RData
+Mouse	27-07-18	mmu	tool-data/l.mmu.up.RData