# HG changeset patch
# User proteore
# Date 1557840530 14400
# Node ID f4e02d20546b4001705ea68edc43e0fcf836abf2
# Parent  4cc2265d1294db685a88a582ffd9b32fb36cdb3a
planemo upload commit c6b2e31fccac66c2caa687b375cbf9947f7ba88e-dirty

diff -r 4cc2265d1294 -r f4e02d20546b kegg_maps_visualization.R
--- a/kegg_maps_visualization.R	Thu Jan 31 05:19:10 2019 -0500
+++ b/kegg_maps_visualization.R	Tue May 14 09:28:50 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
diff -r 4cc2265d1294 -r f4e02d20546b kegg_maps_visualization.xml
--- a/kegg_maps_visualization.xml	Thu Jan 31 05:19:10 2019 -0500
+++ b/kegg_maps_visualization.xml	Tue May 14 09:28:50 2019 -0400
@@ -1,5 +1,5 @@
-<tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2019.01.31">
-    <description>of (differentially expressed) genes/proteins</description>
+<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.05.14">
+    <description>of (differentially expressed) genes/proteins [KEGG]</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
         <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
@@ -69,12 +69,15 @@
                                     <add source="&#x20;" target=""/> 
                                 </mapping>
                                 </sanitizer>
+                                <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
                             </param>
                         </when>
                         <when value="pathways_file">
                             <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
                             <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
-                            <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
+                            <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                                <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                            </param>
                         </when>
                     </conditional>
                 </when>
@@ -103,12 +106,15 @@
                                 <add source="&#x20;" target=""/> 
                             </mapping>
                             </sanitizer>
+                            <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
                         </param>
                     </when>
                     <when value="pathways_file">
                         <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" />
                         <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
-                        <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
+                        <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                            <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                        </param>
                     </when>
                     </conditional>
                 </when>
@@ -137,12 +143,15 @@
                                 <add source="&#x20;" target=""/> 
                             </mapping>
                             </sanitizer>
+                            <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator>
                         </param>
                     </when>
                     <when value="pathways_file">
                         <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" />
                         <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
-                        <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
+                        <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                            <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                        </param>
                     </when>
                     </conditional>
                 </when>
@@ -174,11 +183,15 @@
                 <when value="file" >
                     <param name="file" type="data" format="txt,tabular" 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 if IDs 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="ncol" type="text" value="c1" label="Column if IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'>
+                        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                    </param>
                     <conditional name="foldchange" >
                         <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/>
                             <when value="true">
-                                <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4"/>
+                                <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4">
+                                    <validator type="regex" message="Please enter column numbers, for example: 'c1,c3' for first and third columns">([c]{0,1}[0-9]+[,]*){1,3}</validator>
+                                </param>
                             </when>
                             <when value="false"/>
                     </conditional>