diff id_converter.xml @ 16:b6607b7e683f draft

planemo upload commit f2b3d1ff6bea930b2ce32c009e4d3de39a17edfb-dirty

--- a/id_converter.xml	Tue Dec 18 09:57:21 2018 -0500
+++ b/id_converter.xml	Mon Jan 28 11:08:47 2019 -0500
@@ -1,14 +1,13 @@
-<tool id="IDconverter" name="ID Converter" version="2018.12.18">
+<tool id="IDconverter" name="ID Converter" version="2019.01.28">
     <description>(Human, Mouse, Rat)
     </description>
     <requirements>
-      <requirement type="package" version="3.4.1">R</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
     </stdio>
-    <command interpreter="Rscript">
-        $__tool_directory__/id_converter.R
+    <command><![CDATA[
+        python $__tool_directory__/id_converter.py 
         --id_type="$species.idtypein"
         #if $input.ids == "text"
             --input="$input.txt"
@@ -21,9 +20,9 @@
         #end if
         --target_ids="$species.idto.idtypeout"
         --output="$output"
-        --ref_file="$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.mapping_file ), $__app__.tool_data_tables['proteore_id_mapping'].get_fields() )[0][-1] }"
+        --ref_file="$__tool_directory__/${ filter( lambda x: str( x[2] ) == str( $species.mapping_file ), $__app__.tool_data_tables['proteore_id_mapping'].get_fields() )[0][-1] }"
         
-    </command>
+    ]]></command>
     <inputs>
         <conditional name="input" >
             <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)" >
@@ -55,11 +54,11 @@
         <conditional name="species">
             <param name="mapping_file" type="select" label="Species" >
                 <options from_data_table="proteore_id_mapping"/>
-                <option value="human_id_mapping"></option>
-                <option value="mouse_id_mapping"></option>
-                <option value="rat_id_mapping"></option>
+                <option value="Human"></option>
+                <option value="Mouse"></option>
+                <option value="Rat"></option>
             </param>
-            <when value="human_id_mapping">
+            <when value="Human">
                 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                     <option value="neXtProt" >neXtProt ID (e.g. NX_P31946)</option>
                     <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
@@ -101,7 +100,7 @@
                     </param>
                 </section>
             </when>
-            <when value="mouse_id_mapping">
+            <when value="Mouse">
                 <param name="idtypein" type="select" label="Type/source of IDs" optional="false" >
                     <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                     <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>
@@ -140,7 +139,7 @@
                     </param>
                 </section>
             </when>
-            <when value="rat_id_mapping">
+            <when value="Rat">
                 <param name="idtypein" type="select" label="Select type/source of identifier of your list" optional="false" >
                     <option value="UniProt-AC" selected="True" >UniProt accession number (e.g. P31946)</option>
                     <option value="UniProt-ID" >UniProt ID (e.g 1433B_HUMAN)</option>