Mercurial > repos > devteam > data_manager_sam_fasta_index_builder

diff data_manager/data_manager_sam_fasta_index_builder.xml @ 3:1f54e98616af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:13:56 -0400
parents cf875cbe2df4
children 1865e693d8b2
line wrap: on
line diff
--- a/data_manager/data_manager_sam_fasta_index_builder.xml	Wed Aug 26 13:22:37 2015 -0400
+++ b/data_manager/data_manager_sam_fasta_index_builder.xml	Tue Apr 04 18:13:56 2017 -0400
@@ -3,23 +3,28 @@
     <requirements>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
-    <command interpreter="python">data_manager_sam_fasta_index_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}" --data_table_name "fasta_indexes"</command>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/data_manager_sam_fasta_index_builder.py'
+        '${out_file}'
+        --fasta_filename '${all_fasta_source.fields.path}'
+        --fasta_dbkey '${all_fasta_source.fields.dbkey}'
+        --fasta_description '${all_fasta_source.fields.name}'
+        --data_table_name fasta_indexes
+    ]]></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"/>
     </outputs>
 
     <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>