# HG changeset patch
# User iuc
# Date 1497003122 14400
# Node ID 86e9af693a334847e374207512bf286050b9a3ad
# Parent  ea5faedd0795c551399abeb4a7441dbde6c0ba6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 67d76bc24ec6a5eb145f05416dc2098999897bae

diff -r ea5faedd0795 -r 86e9af693a33 data_manager/bowtie_color_space_index_builder.xml
--- a/data_manager/bowtie_color_space_index_builder.xml	Tue Apr 04 18:06:27 2017 -0400
+++ b/data_manager/bowtie_color_space_index_builder.xml	Fri Jun 09 06:12:02 2017 -0400
@@ -1,32 +1,33 @@
-<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="0.0.3">
+<tool id="bowtie_color_space_index_builder_data_manager" name="Bowtie Color index" tool_type="manage_data" version="1.2.0">
     <description>builder</description>
     <requirements>
-        <requirement type="package" version="1.1.2">bowtie</requirement>
+        <requirement type="package" version="1.2.0">bowtie</requirement>
     </requirements>
-    <command interpreter="python">
-        bowtie_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 "bowtie_indexes_color"
-            --color_space
-    </command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/bowtie_index_builder.py'
+'${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 bowtie_indexes_color
+--color_space
+    ]]></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" help="Leave blank to use all_fasta name" />
-        <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
+        <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
     </outputs>
-    <help>
-
+    <help><![CDATA[
 .. class:: infomark
 
-**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
-
-    </help>
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
+    </citations>
 </tool>
diff -r ea5faedd0795 -r 86e9af693a33 data_manager/bowtie_index_builder.py
--- a/data_manager/bowtie_index_builder.py	Tue Apr 04 18:06:27 2017 -0400
+++ b/data_manager/bowtie_index_builder.py	Fri Jun 09 06:12:02 2017 -0400
@@ -1,4 +1,6 @@
 #!/usr/bin/env python
+from __future__ import print_function
+
 import json
 import optparse
 import os
@@ -42,7 +44,7 @@
     if return_code:
         tmp_stderr.flush()
         tmp_stderr.seek(0)
-        print >> sys.stderr, "Error building index:"
+        print("Error building index:", file=sys.stderr)
         while True:
             chunk = tmp_stderr.read( CHUNK_SIZE )
             if not chunk:
@@ -62,7 +64,6 @@
 
 
 def main():
-    # Parse Command Line
     parser = optparse.OptionParser()
     parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
     parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
diff -r ea5faedd0795 -r 86e9af693a33 data_manager/bowtie_index_builder.xml
--- a/data_manager/bowtie_index_builder.xml	Tue Apr 04 18:06:27 2017 -0400
+++ b/data_manager/bowtie_index_builder.xml	Fri Jun 09 06:12:02 2017 -0400
@@ -1,31 +1,32 @@
-<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="0.0.3">
+<tool id="bowtie_index_builder_data_manager" name="Bowtie index" tool_type="manage_data" version="1.2.0">
     <description>builder</description>
     <requirements>
-        <requirement type="package" version="1.1.2">bowtie</requirement>
+        <requirement type="package" version="1.2.0">bowtie</requirement>
     </requirements>
-    <command interpreter="python">
-        bowtie_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 "bowtie_indexes"
-    </command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/bowtie_index_builder.py'
+'${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 bowtie_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" help="Leave blank to use all_fasta name" />
-        <param type="text" name="sequence_id" value="" label="ID for sequence" help="Leave blank to use all_fasta id "/>
+        <param name="sequence_name" type="text" value="" label="Name of sequence" help="Leave blank to use all_fasta name" />
+        <param name="sequence_id" type="text" value="" label="ID for sequence" help="Leave blank to use all_fasta id" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
     </outputs>
-    <help>
-
+    <help><![CDATA[
 .. class:: infomark
 
-**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
-
-    </help>
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
+    </citations>
 </tool>
diff -r ea5faedd0795 -r 86e9af693a33 tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Tue Apr 04 18:06:27 2017 -0400
+++ b/tool-data/all_fasta.loc.sample	Fri Jun 09 06:12:02 2017 -0400
@@ -4,13 +4,13 @@
 #all_fasta.loc. This file has the format (white space characters are
 #TAB characters):
 #
-#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
 #
 #So, all_fasta.loc could look something like this:
 #
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
 #
 #Your all_fasta.loc file should contain an entry for each individual
 #fasta file. So there will be multiple fasta files for each build,
diff -r ea5faedd0795 -r 86e9af693a33 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 04 18:06:27 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bowtie" version="1.1.2">
-        <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>