# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1372356710 18000
# Node ID 68494d6aabebaed39c2dbdfc529faabbed873183
# Parent  1bc79c9d6165ae82c62d5c9a4c1ab1b1169561c0
Update datamanager and defuse.xml config file generation

diff -r 1bc79c9d6165 -r 68494d6aabeb data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Jun 24 08:12:05 2013 -0500
+++ b/data_manager_conf.xml	Thu Jun 27 13:11:50 2013 -0500
@@ -8,12 +8,14 @@
                 <column name="name" />
                 <column name="path" output_ref="out_file" >  <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
                     <move type="directory"> <!-- Moving a file from the extra files path of "out_file" -->
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/defuse</target> <!-- Target Location to store the file, directories are created as needed -->
+                        !-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/defuse</target> <!-- Target Location to store the file, directories are created as needed -->
                     </move>
                     <!-- datamanager_create_reference.py should have copied the defuse config file to the working directory.  
                          so if we put the ${dbkey}.config path in this column,  defuse.xml can set the data_directory to this this directory.
                      -->
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/defuse/${dbkey}.config</value_translation> <!-- Store this value in the final Data Table -->
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/defuse/${value}.config</value_translation> <!-- Store this value in the final Data Table -->
+                    <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
         </data_table>
diff -r 1bc79c9d6165 -r 68494d6aabeb datamanager_create_reference.xml
--- a/datamanager_create_reference.xml	Mon Jun 24 08:12:05 2013 -0500
+++ b/datamanager_create_reference.xml	Thu Jun 27 13:11:50 2013 -0500
@@ -118,7 +118,7 @@
   </conditional>
  </inputs>
  <outputs>
-  <data name="out_file" format="data_manager_json"/>
+  <data name="out_file" format="data_manager_json" label="${tool.name} : ${genome.ensembl_genome_version}"/>
  </outputs>
   <stdio>
     <exit_code range="1:"  level="fatal"   description="Error running Create DeFuse Reference" />
diff -r 1bc79c9d6165 -r 68494d6aabeb datatypes_conf.xml
--- a/datatypes_conf.xml	Mon Jun 24 08:12:05 2013 -0500
+++ b/datatypes_conf.xml	Thu Jun 27 13:11:50 2013 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <datatypes>
     <registration>
-        <datatype extension="defuse.conf" type="galaxy.datatypes.data:Text" subclass="True"/>
+        <datatype extension="defuse.conf" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="true"/>
     </registration>
 </datatypes>
diff -r 1bc79c9d6165 -r 68494d6aabeb defuse.xml
--- a/defuse.xml	Mon Jun 24 08:12:05 2013 -0500
+++ b/defuse.xml	Thu Jun 27 13:11:50 2013 -0500
@@ -20,7 +20,7 @@
       <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team">
         <options from_file="defuse_reference.loc">
           <column name="name" index="1"/>
-          <column name="value" index="2"/>
+          <column name="value" index="3"/>
           <filter type="sort_by" column="0" />
           <validator type="no_options" message="No indexes are available" />
         </options>
@@ -77,6 +77,9 @@
                but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
   <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
+ <stdio>
+   <exit_code range="1:"  level="fatal" description="Error Running Defuse" />
+ </stdio>
  <outputs>
   <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
   <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
@@ -99,12 +102,11 @@
 #set $ds = chr(36)
 #if $refGenomeSource.genomeSource == "history":
 #set config_file = $refGenomeSource.config.__str__
-#set 
 #else 
 #set config_file = $refGenomeSource.index.value
 #end if
 #set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$'
-#set fh = open()
+#set fh = open($config_file)
 #set keys = ['dataset_directory','ensembl_organism','ensembl_prefix','ensembl_version','ensembl_genome_version','ucsc_genome_version','ncbi_organism','ncbi_prefix','chromosomes','mt_chromosome','gene_sources','ig_gene_sources','rrna_gene_sources']
 #set kv = []
 #for $line in $fh:
@@ -146,18 +148,68 @@
 /project/db/genomes/Hsapiens/hg19/defuse
 #end try
 
+# Organism IDs
+ensembl_organism = #slurp
+#try
+$ref_dict['ensembl_organism']
+#except
+homo_sapiens
+#end try
+
+ensembl_prefix = #slurp
+#try
+$ref_dict['ensembl_prefix']
+#except
+Homo_sapiens
+#end try
+
+ensembl_version = #slurp
+#try
+$ref_dict['ensembl_version']
+#except
+71
+#end try
+
+ensembl_genome_version = #slurp
+#try
+$ref_dict['ensembl_genome_version']
+#except
+GRCh37
+#end try
+
+ucsc_genome_version = #slurp
+#try
+$ref_dict['ucsc_genome_version']
+#except
+hg19
+#end try
+
+ncbi_organism = #slurp
+#try
+$ref_dict['ncbi_organism']
+#except
+Homo_sapiens
+#end try
+
+ncbi_prefix = #slurp
+#try
+$ref_dict['ncbi_prefix']
+#except
+Hs
+#end try
+
 # Input genome and gene models
 gene_models = #slurp
 #try
 $ref_dict['gene_models']
 #except
-\$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf
+\$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf
 #end try
 genome_fasta = #slurp
 #try
 $ref_dict['genome_fasta']
 #except
-\$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa
+\$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa
 #end try
 
 # Repeat table from ucsc genome browser