diff id_converter.xml @ 7:59da262c572c draft

planemo upload commit b260bc0a316c1c74fa88d9b6dbf496127cd31d55-dirty

--- a/id_converter.xml	Fri Mar 23 10:12:01 2018 -0400
+++ b/id_converter.xml	Mon May 28 05:35:49 2018 -0400
@@ -21,7 +21,7 @@
         #end if
         --target_ids="$idto.idtypeout"
         --output="$output"
-        --ref_file="$__tool_directory__/tool-data/human_id_mapping_file.txt"
+        --ref_file="$human_id_mapping"
         
     </command>
     <inputs>
@@ -48,6 +48,12 @@
                 <param name="ncol" type="text" value="c1" label="The column number of 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' />                
             </when>
         </conditional>
+        <param name="human_id_mapping" type="select" label="Select species for ID conversion" >
+            <options from_file="human_id_mapping.loc" >
+                <column name="name" index="1" />
+                <column name="value" index="2" />
+            </options>
+        </param>
 	    <conditional name="idti" >
             <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
 		        <option value="neXtProt_ID" >neXtProt ID (e.g. NX_P31946)</option>
@@ -178,10 +184,10 @@
 
 This tool converts human IDs using the following source files:
 
-* HUMAN_9606_idmapping_selected.tab (Uniprot released on 12/2017)
+* HUMAN_9606_idmapping_selected.tab (Uniprot 15/05/2018)
     Tarball downloaded from ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/
 
-* nextprot_ac_list_all.txt (Nextprot released on 01/08/2017)
+* nextprot_ac_list_all.txt (Nextprot released on 17/01/2018)
     Downloaded from ftp://ftp.nextprot.org/pub/current_release/ac_lists/
 
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