changeset 3:dfceadc0b703 draft

planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty

--- a/kegg_maps_visualization.R	Tue Mar 05 08:32:29 2019 -0500
+++ b/kegg_maps_visualization.R	Fri Jun 28 05:16:30 2019 -0400
@@ -75,6 +75,7 @@
 }
 
 get_list_from_cp <-function(list){
+  list = gsub(";","\t",list)
   list = gsub(",","\t",list)
   list = strsplit(list, "[ \t\n]+")[[1]]
   list = list[list != ""]    #remove empty entry

--- a/kegg_maps_visualization.xml	Tue Mar 05 08:32:29 2019 -0500
+++ b/kegg_maps_visualization.xml	Fri Jun 28 05:16:30 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.03.05">
+<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.06.27.1">
     <description>of (differentially expressed) genes/proteins [KEGG]</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
@@ -39,7 +39,7 @@
     <inputs>
         <!--section name="pathways_section" title="Pathways" expanded="True"--> 
             <conditional name="species">
-                <param name="ref_file" type="select" label="Species" >
+                <param name="ref_file" type="select" label="Species (human, mouse, rat)" >
                     <option value="hsa">Human (Homo sapiens)</option>
                     <option value="mmu">Mouse (Mus musculus)</option>
                     <option value="rno">Rat (Rattus norvegicus)</option>
@@ -200,7 +200,7 @@
         <!--/section-->
         <param name="native" type="select" label="Graphical format">
             <option value="true">KEGG map (.png)</option>
-            <option value="false">Graphviz layout engine (.pdf)</option> 
+            <option value="false">KEGG map, graphviz layout engine (.pdf)</option> 
         </param>
     </inputs>
     <outputs>
@@ -246,7 +246,7 @@
 
 **Description**
 
-This tool based on the Pathview R package, is set for pathway based data integration and visualization. 
+This tool, relying on the Pathview R package, is set for pathway based data integration and visualization. 
 
 It maps and renders a wide variety of biological data on relevant KEGG pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data.
 
@@ -277,24 +277,24 @@
 If there's more than one ID per line in the specified column, it will be splitted resulting in one unique ID per line. For example this table:
 
 .. csv-table:: Simulated data
-   :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
+   :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
 
-    "ENSG00000136881","Q14032","BAAT_HUMAN"
-    "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000244731","P0C0L4","CO4A_HUMAN"
+    "6881","Q14032","BAAT_HUMAN"
+    "70099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "731","P0C0L4","CO4A_HUMAN"
 
 |
 
 will be converted as follow:
 
 .. csv-table:: Simulated data
-   :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
+   :header: "Entrez_gene_ID","UniProt.AC","UniProt.ID"
 
-    "ENSG00000136881","Q14032","BAAT_HUMAN"
-    "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
-    "ENSG00000244731","P0C0L4","CO4A_HUMAN"
+    "6881","Q14032","BAAT_HUMAN"
+    "70099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "70099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "70099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
+    "731","P0C0L4","CO4A_HUMAN"
 
 |
 
@@ -302,7 +302,7 @@
 
 **Output:**
 
-- a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
+- a set of graphical map, i.e. a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each KEGG map.
 
 - a **summary text file** (.tsv) of the mapping(s) with the following columns
     - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
@@ -345,7 +345,7 @@
 
 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
 
-Contact [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
+Help: [e-mail] for any questions or concerns about this tool.
     ]]></help>
     <citations>
         <citation type="doi">10.1093/nar/gkx372</citation>