# HG changeset patch
# User iuc
# Date 1569966750 14400
# Node ID 0beac6016b4103ed31d2cd51486e2cfde8536600
# Parent  2ee9ab762320b2d1537821db58dd291f7d208630
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 823259bba9405d22dc2add24746057122c819ad3"

diff -r 2ee9ab762320 -r 0beac6016b41 data_manager/bwameth_index_builder.py
--- a/data_manager/bwameth_index_builder.py	Tue Apr 04 17:49:45 2017 -0400
+++ b/data_manager/bwameth_index_builder.py	Tue Oct 01 17:52:30 2019 -0400
@@ -24,7 +24,7 @@
     if return_code:
         print >> sys.stderr, "Error building index."
         sys.exit( return_code )
-    data_table_entry = dict(value=args.dbKey, dbkey=args.dbkey, name=args.name, path=args.dbKey)
+    data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename)
     _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
 
 
diff -r 2ee9ab762320 -r 0beac6016b41 data_manager/bwameth_index_builder.xml
--- a/data_manager/bwameth_index_builder.xml	Tue Apr 04 17:49:45 2017 -0400
+++ b/data_manager/bwameth_index_builder.xml	Tue Oct 01 17:52:30 2019 -0400
@@ -1,53 +1,51 @@
-<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0">
+<tool id="bwameth_index_builder_data_manager" name="bwa-meth index" tool_type="manage_data" version="1.0.0.1">
     <description>builder</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.2.2</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.7.12">bwa</requirement>
-        <requirement type="package" version="1.2">samtools</requirement>
-        <requirement type="package" version="0.2.0">bwameth</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bwameth</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        #if str($sequence_id).strip() != "":
-            #set $dbkey = $sequence_id
-        #else:
-            #set $dbkey = $all_fasta_source.fields.dbkey
-        #end if
+#if str($sequence_id).strip():
+    #set $dbkey = $sequence_id
+#else:
+    #set $dbkey = $all_fasta_source.fields.dbkey
+#end if
 
-        #if str($sequence_name).strip() != "":
-            #set $name = $sequence_name
-        #else:
-            #set $name = $all_fasta_source.fields.name
-        #end if
+#if str($sequence_name).strip():
+    #set $name = $sequence_name
+#else:
+    #set $name = $all_fasta_source.fields.name
+#end if
 
-        python $__tool_directory__/bwameth_index_builder.py --output "${out_file}" 
-            --fasta_filename "${all_fasta_source.fields.path}" 
-            --dbkey "${dbkey}"
-            --name "${name}" 
-            --data_table_name "bwameth_indexes"
-        ]]>
-    </command>
+python '$__tool_directory__/bwameth_index_builder.py' --output '${out_file}'
+--fasta_filename '${all_fasta_source.fields.path}'
+--dbkey '${dbkey}'
+--name '${name}'
+--data_table_name bwameth_indexes
+    ]]></command>
     <inputs>
-        <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
             <options from_data_table="all_fasta" />
         </param>
-        <param label="ID for index" name="sequence_id" type="text" value="" help="If not specified, the value from the fasta file is used"/>
-        <param label="Displayed description for sequence" name="sequence_name" type="text" value="" help="If not specified, the value from the fasta file is used"/>
+        <param name="sequence_id" type="text" value="" label="ID for index" help="If not specified, the value from the fasta file is used"/>
+        <param name="sequence_name" type="text" value="" label="Displayed description for sequence" help="If not specified, the value from the fasta file is used"/>
     </inputs>
     <outputs>
-        <data format="data_manager_json" name="out_file" />
+        <data name="out_file" format="data_manager_json" />
     </outputs>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 .. 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.
 
 What is BWA-meth?
 -----------------
 
 BWA-meth performs alignment of reads in a bisulfite-sequencing experiment (e.g., RRBS or WGBS) to a genome. The methodology employed for this is similar to bismark, where both the reads and the reference genome are *in silico* converted prior to alignment. Methylation extraction on the resulting BAM file can be done with the PileOMeth tool.
 
-]]>
-    </help>
+    ]]></help>
     <citations>
         <citation type="bibtex">@misc{1401.1129,
         Author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz},
diff -r 2ee9ab762320 -r 0beac6016b41 data_manager_conf.xml
--- a/data_manager_conf.xml	Tue Apr 04 17:49:45 2017 -0400
+++ b/data_manager_conf.xml	Tue Oct 01 17:52:30 2019 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager/bwameth_index_builder.xml" id="bwameth_index_builder" version="0.0.1">
+    <data_manager tool_file="data_manager/bwameth_index_builder.xml" id="bwameth_index_builder">
         <data_table name="bwameth_indexes">
             <output>
                 <column name="value" />
diff -r 2ee9ab762320 -r 0beac6016b41 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 04 17:49:45 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="bwa" version="0.7.12">
-       <repository changeset_revision="67aa12c8d449" name="package_bwa_0_7_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="1.2">
-       <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bwameth" version="0.2.0">
-        <repository changeset_revision="fd470f9ef129" name="package_python_2_7_bwameth_0_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>