# HG changeset patch
# User devteam
# Date 1444745911 14400
# Node ID bb4185c65cc7e52222cbe45d1269bbc8afdd7a08
# Parent  e09681f51de478c83b7f07de4a59e4d948d6f8d7
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r e09681f51de4 -r bb4185c65cc7 data_manager/data_manager_gatk_picard_index_builder.py
--- a/data_manager/data_manager_gatk_picard_index_builder.py	Fri Apr 04 15:43:20 2014 -0400
+++ b/data_manager/data_manager_gatk_picard_index_builder.py	Tue Oct 13 10:18:31 2015 -0400
@@ -27,27 +27,16 @@
             sequence_name = dbkey
     return sequence_id, sequence_name
 
-def build_picard_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id,
-                        sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME, sort_fasta=False,
-                        sam_index_path=None ):
+def build_picard_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME ):
     fasta_base_name = os.path.split( fasta_filename )[-1]
-    fasta_to_index = os.path.join( target_directory, fasta_base_name )
-    if sort_fasta:
-        shutil.copy( fasta_filename, fasta_to_index )
-        _sort_fasta_gatk( fasta_to_index )
-    else:
-        os.symlink(fasta_filename, fasta_to_index)
-    sam_index_filename = '%s.fai' % fasta_base_name
-    if sam_index_path is not None:
-        sam_index_basepath = os.path.split( sam_index_path )[0]
-    else:
-        sam_index_basepath = os.path.join( target_directory, sam_index_filename )
-    if sam_index_path is not None and os.path.exists( sam_index_path ) and os.path.exists( os.path.join( sam_index_basepath, sam_index_filename ) ):
-        os.symlink( sam_index_path + '.fai', os.path.join( target_directory, sam_index_filename ) )
-    else:
-        sam_command = [ 'samtools', 'faidx', fasta_to_index ]
+    gatk_sorted_fasta_filename = os.path.join( target_directory, fasta_base_name )
+    shutil.copy( fasta_filename, gatk_sorted_fasta_filename )
+    _sort_fasta_gatk( gatk_sorted_fasta_filename )
+    sam_index_filename = '%s.fai' % gatk_sorted_fasta_filename
+    if not os.path.exists( sam_index_filename ):
+        sam_command = [ 'samtools', 'faidx', gatk_sorted_fasta_filename ]
         _run_command( sam_command, target_directory )
-    args = [ 'java', '-jar', jar, 'R=%s' % fasta_to_index, 'O=%s.dict' % sequence_id ]
+    args = [ 'java', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ]
     _run_command( args, target_directory )
     data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
     _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
@@ -160,8 +149,6 @@
     parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
     parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
     parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", default=None, help='GATK .jar file' )
-    parser.add_option( '-s', '--sort_fasta', dest='sort_fasta', action='store', type="string", default=False, help='Sort input FASTA' )
-    parser.add_option( '-i', '--sam_index', dest='sam_index', action='store', type="string", default=None, help='SAM index of input FASTA' )
     (options, args) = parser.parse_args()
     
     filename = args[0]
@@ -183,9 +170,7 @@
                         options.fasta_dbkey, 
                         sequence_id, 
                         sequence_name, 
-                        options.jar,
-                        sort_fasta=options.sort_fasta,
-                        sam_index_path=options.sam_index,
+                        options.jar, 
                         data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
     
     #save info to json file
diff -r e09681f51de4 -r bb4185c65cc7 data_manager/data_manager_gatk_picard_index_builder.xml
--- a/data_manager/data_manager_gatk_picard_index_builder.xml	Fri Apr 04 15:43:20 2014 -0400
+++ b/data_manager/data_manager_gatk_picard_index_builder.xml	Tue Oct 13 10:18:31 2015 -0400
@@ -1,46 +1,28 @@
-<tool id="gatk_picard_index_builder" name="Generate Picard indexes" tool_type="manage_data" version="0.0.2">
-    <description>sorted for GATK</description>
+<tool id="gatk_picard_index_builder" name="Generate GATK-sorted Picard indexes" tool_type="manage_data" version="0.0.1">
+    <description>builder</description>
     <requirements>
         <requirement type="package" version="0.1.18">samtools</requirement>
         <requirement type="package" version="1.56.0">picard</requirement>
     </requirements>
     <command interpreter="python">
-        data_manager_gatk_picard_index_builder.py "${out_file}" \
-            --jar "\$JAVA_JAR_PATH/CreateSequenceDictionary.jar" \
-            --fasta_filename "${all_fasta_source.fields.path}" \
-            --fasta_dbkey "${all_fasta_source.fields.dbkey}" \
-            --fasta_description "${all_fasta_source.fields.name}" \
-            #if $input_fasta_sorting.sort_input_fasta == 'sort_fasta':
-                --sort_fasta \
-            #else:
-                --sam_index "${input_fasta_sorting.sam_index_source.fields.path}" \
-            #end if 
+        data_manager_gatk_picard_index_builder.py "${out_file}"
+            --jar "\$JAVA_JAR_PATH/CreateSequenceDictionary.jar"
+            --fasta_filename "${all_fasta_source.fields.path}"
+            --fasta_dbkey "${all_fasta_source.fields.dbkey}"
+            --fasta_description "${all_fasta_source.fields.name}"
             --data_table_name "gatk_picard_indexes"
     </command>
     <inputs>
         <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
-            <options from_data_table="all_fasta" />
+            <options from_data_table="all_fasta"/>
         </param>
-        <conditional name="input_fasta_sorting">
-            <param name="sort_input_fasta" type="select" label="Input fasta sorting">
-                <option value="input_order" selected="True">As-is</option>
-                <option value="sort_fasta">Sort for GATK</option>
-            </param>
-            <when value="input_order">
-                <param name="sam_index_source" type="select" label="SAM index of FASTA">
-                    <options from_data_table="fasta_indexes">
-                        <filter type="param_value" column="0" key="value" ref="all_fasta_source" />
-                        <validator type="no_options" message="This FASTA file does not have SAM indexes."/>
-                    </options>
-                </param>
-            </when>
-        </conditional>
         <param type="text" name="sequence_name" value="" label="Name of sequence" />
         <param type="text" name="sequence_id" value="" label="ID for sequence" />
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json"/>
     </outputs>
+
     <help>
 
 .. class:: infomark
diff -r e09681f51de4 -r bb4185c65cc7 tool-data/fasta_indexes.loc.sample
--- a/tool-data/fasta_indexes.loc.sample	Fri Apr 04 15:43:20 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a fasta_indexes.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The fasta_indexes.loc
-#file has this format (white space characters are TAB characters):
-#
-# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
-#
-#So, for example, if you had hg19 Canonical indexed stored in
-#
-# /depot/data2/galaxy/hg19/sam/,
-#
-#then the fasta_indexes.loc entry would look like this:
-#
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#
-#and your /depot/data2/galaxy/hg19/sam/ directory
-#would contain hg19canon.fa and hg19canon.fa.fai files.
-#
-#Your fasta_indexes.loc file should include an entry per line for
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
-#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r e09681f51de4 -r bb4185c65cc7 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Apr 04 15:43:20 2014 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Oct 13 10:18:31 2015 -0400
@@ -10,9 +10,4 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gatk_sorted_picard_index.loc" />
     </table>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="fasta_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/fasta_indexes.loc" />
-    </table>
 </tables>
diff -r e09681f51de4 -r bb4185c65cc7 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Apr 04 15:43:20 2014 -0400
+++ b/tool_dependencies.xml	Tue Oct 13 10:18:31 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="picard" version="1.56.0">
-      <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="7206dbf34dcd" name="package_picard_1_56_0" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
-      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>