diff data_manager/bowtie2_index_builder.xml @ 3:83da94c0e4a6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f

--- a/data_manager/bowtie2_index_builder.xml	Mon Nov 16 15:20:08 2015 -0500
+++ b/data_manager/bowtie2_index_builder.xml	Tue Apr 04 18:06:10 2017 -0400
@@ -1,30 +1,31 @@
-<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.2.6">
+<tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.3.0">
     <description>builder</description>
     <requirements>
-        <requirement type="package" version="2.2.6">bowtie2</requirement>
+        <requirement type="package" version="2.3.0">bowtie2</requirement>
     </requirements>
-    <command interpreter="python">bowtie2_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 "bowtie2_indexes" ${tophat2}</command>
-    <stdio>
-        <exit_code range=":-1" />
-        <exit_code range="1:" />
-    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/bowtie2_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 bowtie2_indexes ${tophat2}
+    ]]></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 type="boolean" name="tophat2" label="Also make available for TopHat" checked="True" truevalue="--data_table_name tophat2_indexes" falsevalue="" help="Adds values to tophat2_indexes tool data table." />
+        <param name="sequence_name" type="text" value="" label="Name of sequence" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" />
+        <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" />
     </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>