diff data_manager/twobit_builder.xml @ 2:9946bc39c834 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f

--- a/data_manager/twobit_builder.xml	Thu Jan 19 11:45:43 2017 -0500
+++ b/data_manager/twobit_builder.xml	Tue Apr 04 18:16:29 2017 -0400
@@ -3,14 +3,19 @@
         <requirement type="package" version="324">ucsc-fatotwobit</requirement>
     </requirements>
     <description>builder</description>
-    <command interpreter="python">twobit_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}"</command>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/twobit_builder.py'
+        '${out_file}'
+        --fasta_filename '${all_fasta_source.fields.path}'
+        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+        --fasta_description '${all_fasta_source.fields.name}'
+    ]]></command>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta"/>
         </param>
-        <param type="text" name="sequence_name" value="" label="Name of sequence" />
-        <param type="text" name="sequence_id" value="" label="ID for sequence" />
-        
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
@@ -25,11 +30,9 @@
     </tests>
 
     <help>
-
 .. class:: infomark
 
-**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
-
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
     </help>
 </tool>