# HG changeset patch
# User proteore
# Date 1536933148 14400
# Node ID 6d5c0ff2b0bd10c08788365d600132b095a71a93
# Parent  e8d6e50f5d38e4fef5a1d92a134b20f0a40f14ab
planemo upload commit 3cfb63ac3585431e7cdcc0a0bd11c33b946a6751-dirty

diff -r e8d6e50f5d38 -r 6d5c0ff2b0bd Pathview.xml
--- a/Pathview.xml	Thu Sep 13 03:25:04 2018 -0400
+++ b/Pathview.xml	Fri Sep 14 09:52:28 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.09.13">
+<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.09.14">
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
     </requirements>
@@ -38,56 +38,7 @@
 
     ]]></command>
     <inputs>
-        <param name="id_type" type="select" label="Select your identifiers type :">
-            <option value="uniprotID">Uniprot Accession number</option>
-            <option value="geneID">Entrez gene ID</option>
-        </param>
-        <conditional name="input" >
-            <param name="ids" type="select" label="Provide your identifiers" 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>
-            <when value="text" >
-                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
-                    <sanitizer invalid_char=''>
-                        <valid initial="string.printable">
-                            <remove value="&apos;"/>
-                        </valid>
-                        <mapping initial="none">
-                            <add source="&apos;" target="__sq__"/>
-                        </mapping>
-                    </sanitizer>
-                </param>
-            </when>
-            <when value="file" >
-                <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
-                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
-                <param name="ncol" type="text" value="c1" label="The column which contains your 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' />
-                <conditional name="expression_values">
-                    <param name="nb_exp" type="select" label="How many expression values column in your file ?">
-                        <option value="0" >0</option>
-                        <option value="1" >1</option>
-                        <option value="2" >2</option>
-                        <option value="3" >3</option>
-                    </param>
-                    <when value="0">
-                    </when>
-                    <when value="1">
-                        <param name="e1" type="text" value="" label="First column number of your expression data" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'/>
-                    </when>
-                    <when value="2">
-                        <param name="e1" type="text" value="" label="First column number of your expression data"/>
-                        <param name="e2" type="text" value="" label="Second column number of your expression data"/>
-                    </when>
-                    <when value="3">
-                        <param name="e1" type="text" value="" label="First column number of your expression data"/>
-                        <param name="e2" type="text" value="" label="Second column number of your expression data"/>
-                        <param name="e3" type="text" value="" label="Third column number of your expression data"/>
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
-        <conditional name="species">
+    <conditional name="species">
         <param name="ref_file" type="select" label="Select species" >
             <option value="hsa">Human (hsa)</option>
             <option value="mmu">Mouse (mmu)</option>
@@ -161,6 +112,55 @@
                 </conditional>
             </when>
         </conditional>
+        <param name="id_type" type="select" label="Select your identifiers type :">
+            <option value="uniprotID">Uniprot Accession number</option>
+            <option value="geneID">Entrez gene ID</option>
+        </param>
+        <conditional name="input" >
+            <param name="ids" type="select" label="Provide your identifiers" 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>
+            <when value="text" >
+                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by "," into the form field, for example: P31946,P62258' >
+                    <sanitizer invalid_char=''>
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="__sq__"/>
+                        </mapping>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="file" >
+                <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" />
+                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" />
+                <param name="ncol" type="text" value="c1" label="The column which contains your 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' />
+                <conditional name="expression_values">
+                    <param name="nb_exp" type="select" label="How many expression values column in your file ?">
+                        <option value="0" >0</option>
+                        <option value="1" >1</option>
+                        <option value="2" >2</option>
+                        <option value="3" >3</option>
+                    </param>
+                    <when value="0">
+                    </when>
+                    <when value="1">
+                        <param name="e1" type="text" value="" label="First column number of your expression data" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'/>
+                    </when>
+                    <when value="2">
+                        <param name="e1" type="text" value="" label="First column number of your expression data"/>
+                        <param name="e2" type="text" value="" label="Second column number of your expression data"/>
+                    </when>
+                    <when value="3">
+                        <param name="e1" type="text" value="" label="First column number of your expression data"/>
+                        <param name="e2" type="text" value="" label="Second column number of your expression data"/>
+                        <param name="e3" type="text" value="" label="Third column number of your expression data"/>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
         <param name="native" type="select" label="Choose the output graph format">
             <option value="true">KEGG graph (.png)</option>
             <option value="false">Graphviz layout engine (.pdf)</option>