diff add_protein_features.xml @ 12:1a4cfa7a3a27 draft

planemo upload commit 77279e994f5751c6cd9aa165aa0604db3d241271-dirty

--- a/add_protein_features.xml	Fri Jan 18 04:13:47 2019 -0500
+++ b/add_protein_features.xml	Mon Mar 11 09:16:00 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="prot_features" name="Add protein features" version="2019.01.18">
+<tool id="prot_features" name="Add protein features" version="2019.03.11">
 <description>[neXtProt]
 </description>
 <requirements>
@@ -23,7 +23,12 @@
   --localization='$Nextprot_params.localization' 
   --diseases_info='$Nextprot_params.diseases_info'  
   --output='$output'  
-  --nextprot=$__tool_directory__/tool-data/result_nextprot.txt 
+
+  #if 'nextprot_ref' in str($ref_file).split("/")
+    --nextprot="$ref_file" 
+  #else 
+    --nextprot="$__tool_directory__/$ref_file"
+  #end if 
     
 ]]></command>
 
@@ -51,9 +56,10 @@
     </when>
     <when value="file">
       <param name="genelist" type="data" format="txt,tabular" label="Select your file" help=""/>
-      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1"/> 
+      <param name="column" type="text" label="Column IDs (e.g : Enter c1 for column n°1)" value="c1">
+        <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+      </param>
       <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does input file have header?" />
-
     </when>
   </conditional>
 
@@ -62,7 +68,7 @@
           <option value="NextprotID" selected="false">neXtProt IDs</option>
       </param>
       <section name="Nextprot_params" title="Select features" expanded="True">
-        <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="true"> 
+        <param name="pc_features" type="select" label="Physico-Chemical Features" multiple="true" help="" display="checkboxes" optional="false"> 
           <option value="SeqLength" selected="false">Sequence Length</option>
           <option value="MW" selected="false">Molecular Weight</option>
           <option value="IsoPoint" selected="false">Isoelectric point</option>
@@ -78,6 +84,9 @@
         <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" />
 
       </section>
+      <param name="ref_file" type="select" label="Release of neXtProt reference file to use">
+        <options from_data_table="proteore_nextprot_ref"/>
+      </param>
 
 </inputs>