--- a/defuse.xml	Sat Jun 15 14:36:47 2013 -0500
+++ b/defuse.xml	Fri Jun 21 14:46:11 2013 -0500
@@ -12,66 +12,66 @@
   <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads.  (FASTQ interlacer will pair reads and remove the unpaired.   FASTQ de-interlacer will separate the result into left and right reads.)"/>
   <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
   <conditional name="refGenomeSource">
-      <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
-        <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
-        <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
+    <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
+      <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
+      <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
+    </param>
+    <when value="indexed">
+      <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"/>
+          <filter type="sort_by" column="0" />
+          <validator type="no_options" message="No indexes are available" />
+        </options>
       </param>
-      <when value="indexed">
-        <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.loc">
-            <column name="name" index="1"/>
-            <column name="value" index="2"/>
-            <filter type="sort_by" column="0" />
-            <validator type="no_options" message="No indexes are available" />
-          </options>
-        </param>
-        <conditional name="defuse_param">
-          <param name="settings" type="select" label="Defuse parameter settings" help="">
-            <option value="preSet">Default settings</option>
-            <option value="full">Full parameter list</option>
-          </param>
-          <when value="preSet" />
-          <when value="full">
-            <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
-            <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
-            <param name="discord_read_trim" type="integer" value="50" optional="true" label="Trim length for discordant reads discord_read_trim" help="(split reads are not trimmed)" />
-            <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
-              <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
-            </param>
-            <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
-            <param name="split_count_threshold" type="integer" value="3" optional="true" label="Filter split_count_threshold" />
-            <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
-              <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
-            </param>
-            <param name="max_dist_pos" type="integer" value="600" optional="true" label="Filter max_dist_pos" />
-            <param name="num_dist_genes" type="integer" value="500" optional="true" label="Filter num_dist_genes" />
-            <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
-            <param name="max_concordant_ratio" type="float" value="0.1" optional="true" label="Filter max_concordant_ratio">
-              <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
-            </param>
-            <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
-            <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
-              <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
-            </param>
-            <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
-              <help>Position density when calculating covariance</help>
-              <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
-            </param>
-            <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
-              <option value="">Use Default</option>
-              <option value="no">no</option>
-              <option value="yes">yes</option>
-            </param>
-            <!--
-              <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
-            -->
-          </when> <!-- full -->
-        </conditional>  <!-- defuse_param -->
-      </when>
-      <when value="history">
-        <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
-      </when>  <!-- history -->
+    </when>
+    <when value="history">
+      <param name="config" type="data" format="defuse.conf" label="Defuse Config file" help=""/>
+    </when>  <!-- history -->
   </conditional>  <!-- refGenomeSource -->
+  <conditional name="defuse_param">
+    <param name="settings" type="select" label="Defuse parameter settings" help="">
+      <option value="preSet">Default settings</option>
+      <option value="full">Full parameter list</option>
+    </param>
+    <when value="preSet" />
+    <when value="full">
+      <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
+      <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
+      <param name="discord_read_trim" type="integer" value="50" optional="true" label="Trim length for discordant reads discord_read_trim" help="(split reads are not trimmed)" />
+      <param name="calculate_extra_annotations" type="select" label="Calculate extra annotations, fusion splice index and interrupted index" help="">
+        <option value="">Use Default</option>
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
+        <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
+      </param>
+      <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
+      <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
+        <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
+      </param>
+      <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
+      <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
+      <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
+        <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
+      </param>
+      <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
+        <help>Position density when calculating covariance</help>
+        <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
+      </param>
+      <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
+        <option value="">Use Default</option>
+        <option value="no">no</option>
+        <option value="yes">yes</option>
+      </param>
+      <!--
+        <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
+      -->
+      <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" />
+    </when> <!-- full -->
+  </conditional>  <!-- defuse_param -->
   <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
          help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
                but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
@@ -83,20 +83,50 @@
   <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">
     <filter>keep_output == True</filter>
   </data>
-  <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" />
   <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
   <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
   <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
     <filter>do_get_reads == True</filter>
   </data>
+  <!--
+   expression_plot
+   circos plot
+  -->
  </outputs>
  <configfiles>
   <configfile name="defuse_config">
-#import ast
+#import re
+#set $ds = chr(36)
 #if $refGenomeSource.genomeSource == "history":
-#include raw $refGenomeSource.config.__str__
+#set config_file = $refGenomeSource.config.__str__
+#set 
 #else 
-#set $ref_dict = dict($ast.literal_eval($refGenomeSource.index.value))
+#set config_file = $refGenomeSource.index.value
+#end if
+#set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$'
+#set fh = open()
+#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:
+  #set m = $re.match($pat,$line)
+  #if $m and len($m.groups()) == 2:
+    ## #echo $line
+    #if $m.groups()[0] in keys:
+      #set k = $m.groups()[0]
+      #if k == 'dataset_directory' and $refGenomeSource.genomeSource == "indexed":
+        ## The DataManager is conifgured to place the config file in the same directory as the defuse_data: dataset_directory
+        #set v = $os.path.dirname($config_file)
+      #else:
+        #set v = $m.groups()[1]
+      #end if
+      #set kv = $kv + [[$k, $v]]
+    #end if
+  #end if
+#end for
+## #echo $kv
+#set ref_dict = dict($kv)
+## #echo $ref_dict
+## include raw $refGenomeSource.config.__str__
 #
 # Configuration file for defuse
 #
@@ -106,12 +136,7 @@
 # Directory where the defuse code was unpacked
 ## Default location in the tool/defuse directory  
 # source_directory = ${__root_dir__}/tools/defuse
-source_directory = #slurp
-#try
-$ref_dict['source_directory']
-#except
-__DEFUSE_PATH__
-#end try
+source_directory = __DEFUSE_PATH__
 
 # Directory where you want your dataset
 dataset_directory = #slurp
@@ -166,60 +191,15 @@
 #end try
 
 # Paths to external tools
-bowtie_bin = #slurp
-#try
-$ref_dict['bowtie_bin']
-#except
-__BOWTIE_BIN__
-#end try
-bowtie_build_bin = #slurp
-#try
-$ref_dict['bowtie_build_bin']
-#except
-__BOWTIE_BUILD_BIN__
-#end try
-blat_bin = #slurp
-#try
-$ref_dict['blat_bin']
-#except
-__BLAT_BIN__
-#end try
-fatotwobit_bin = #slurp
-#try
-$ref_dict['fatotwobit_bin']
-#except
-__FATOTWOBIT_BIN__
-#end try
-gmap_bin = #slurp
-#try
-$ref_dict['gmap_bin']
-#except
-__GMAP_BIN__
-#end try
-gmap_bin = #slurp
-#try
-$ref_dict['gmap_bin']
-#except
-__GMAP_BIN__
-#end try
-gmap_setup_bin = #slurp
-#try
-$ref_dict['gmap_setup_bin']
-#except
-__GMAP_SETUP_BIN__
-#end try
-r_bin = #slurp
-#try
-$ref_dict['r_bin']
-#except
-__R_BIN__
-#end try
-rscript_bin = #slurp
-#try
-$ref_dict['rscript_bin']
-#except
-__RSCRIPT_BIN__
-#end try
+bowtie_bin = __BOWTIE_BIN__
+bowtie_build_bin = __BOWTIE_BUILD_BIN__
+blat_bin = __BLAT_BIN__
+fatotwobit_bin = __FATOTWOBIT_BIN__
+gmap_bin = __GMAP_BIN__
+gmap_bin = __GMAP_BIN__
+gmap_setup_bin = __GMAP_SETUP_BIN__
+r_bin = __R_BIN__
+rscript_bin = __RSCRIPT_BIN__
 
 # Directory where you want your dataset
 gmap_index_directory = #slurp
@@ -284,8 +264,8 @@
 --phred33-quals
 #end try
 max_insert_size = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_insert_size.__str__ != "":
-$refGenomeSource.defuse_param.max_insert_size
+#if $defuse_param.settings == "full" and $defuse_param.max_insert_size.__str__ != "":
+$defuse_param.max_insert_size
 #else
 #try
 $ref_dict['max_insert_size']
@@ -336,8 +316,8 @@
 
 # Minimum gene fusion range
 dna_concordant_length = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.dna_concordant_length.__str__ != "":
-$refGenomeSource.defuse_param.dna_concordant_length
+#if $defuse_param.settings == "full" and $defuse_param.dna_concordant_length.__str__ != "":
+$defuse_param.dna_concordant_length
 #else
 #try
 $ref_dict['dna_concordant_length']
@@ -348,8 +328,8 @@
 
 # Trim length for discordant reads (split reads are not trimmed)
 discord_read_trim = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.discord_read_trim.__str__ != "":
-$refGenomeSource.defuse_param.discord_read_trim
+#if $defuse_param.settings == "full" and $defuse_param.discord_read_trim.__str__ != "":
+$defuse_param.discord_read_trim
 #else
 #try
 $ref_dict['discord_read_trim']
@@ -357,11 +337,21 @@
 50
 #end try
 #end if
-
+# Calculate extra annotations, fusion splice index and interrupted index
+calculate_extra_annotations = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.calculate_extra_annotations.__str__ != "":
+$defuse_param.calculate_extra_annotations
+#else
+#try
+$ref_dict['calculate_extra_annotations']
+#except
+no
+#end try
+#end if
 # Filtering parameters
 clustering_precision = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.clustering_precision.__str__ != ""
-$refGenomeSource.defuse_param.clustering_precision
+#if $defuse_param.settings == "full" and $defuse_param.clustering_precision.__str__ != ""
+$defuse_param.clustering_precision
 #else
 #try
 $ref_dict['clustering_precision']
@@ -370,8 +360,8 @@
 #end try
 #end if
 span_count_threshold = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.span_count_threshold.__str__ != ""
-$refGenomeSource.defuse_param.span_count_threshold
+#if $defuse_param.settings == "full" and $defuse_param.span_count_threshold.__str__ != ""
+$defuse_param.span_count_threshold
 #else
 #try
 $ref_dict['span_count_threshold']
@@ -379,19 +369,9 @@
 5
 #end try
 #end if
-split_count_threshold = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_count_threshold.__str__ != ""
-$refGenomeSource.defuse_param.split_count_threshold
-#else
-#try
-$ref_dict['split_count_threshold']
-#except
-3
-#end try
-#end if
 percent_identity_threshold = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.percent_identity_threshold.__str__ != ""
-$refGenomeSource.defuse_param.percent_identity_threshold
+#if $defuse_param.settings == "full" and $defuse_param.percent_identity_threshold.__str__ != ""
+$defuse_param.percent_identity_threshold
 #else
 #try
 $ref_dict['percent_identity_threshold']
@@ -399,29 +379,9 @@
 0.90
 #end try
 #end if
-max_dist_pos = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_dist_pos.__str__ != ""
-$refGenomeSource.defuse_param.max_dist_pos
-#else
-#try
-$ref_dict['max_dist_pos']
-#except
-600
-#end try
-#end if
-num_dist_genes = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.num_dist_genes.__str__ != ""
-$refGenomeSource.defuse_param.num_dist_genes
-#else
-#try
-$ref_dict['num_dist_genes']
-#except
-500
-#end try
-#end if
 split_min_anchor = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_min_anchor.__str__ != ""
-$refGenomeSource.defuse_param.split_min_anchor
+#if $defuse_param.settings == "full" and $defuse_param.split_min_anchor.__str__ != ""
+$defuse_param.split_min_anchor
 #else
 #try
 $ref_dict['split_min_anchor']
@@ -429,19 +389,9 @@
 4
 #end try
 #end if
-max_concordant_ratio = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_concordant_ratio.__str__ != ""
-$refGenomeSource.defuse_param.max_concordant_ratio
-#else
-#try
-$ref_dict['max_concordant_ratio']
-#except
-0.1
-#end try
-#end if
 splice_bias = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.splice_bias.__str__ != ""
-$refGenomeSource.defuse_param.splice_bias
+#if $defuse_param.settings == "full" and $defuse_param.splice_bias.__str__ != ""
+$defuse_param.splice_bias
 #else
 #try
 $ref_dict['splice_bias']
@@ -450,8 +400,8 @@
 #end try
 #end if
 denovo_assembly = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.denovo_assembly.__str__ != ""
-$refGenomeSource.defuse_param.denovo_assembly
+#if $defuse_param.settings == "full" and $defuse_param.denovo_assembly.__str__ != ""
+$defuse_param.denovo_assembly
 #else
 #try
 $ref_dict['denovo_assembly']
@@ -460,8 +410,8 @@
 #end try
 #end if
 probability_threshold = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.probability_threshold.__str__ != ""
-$refGenomeSource.defuse_param.probability_threshold
+#if $defuse_param.settings == "full" and $defuse_param.probability_threshold.__str__ != ""
+$defuse_param.probability_threshold
 #else
 #try
 $ref_dict['probability_threshold']
@@ -473,8 +423,8 @@
 
 # Position density when calculating covariance
 covariance_sampling_density = #slurp
-#if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.covariance_sampling_density.__str__ != ""
-$refGenomeSource.defuse_param.covariance_sampling_density
+#if $defuse_param.settings == "full" and $defuse_param.covariance_sampling_density.__str__ != ""
+$defuse_param.covariance_sampling_density
 #else
 #try
 $ref_dict['covariance_sampling_density']
@@ -482,13 +432,17 @@
 0.01
 #end try
 #end if
-
-
 # Number of reads for each job in split
-reads_per_job                               = 1000000
-
-# Number of regions for each breakpoint sequence job in split
-regions_per_job                             = 20
+reads_per_job = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.reads_per_job.__str__ != ""
+$defuse_param.reads_per_job
+#else
+#try
+$ref_dict['reads_per_job']
+#except
+1000000
+#end try
+#end if
 
 #raw
 # If you have command line 'mail' and wish to be notified
@@ -498,40 +452,8 @@
 remove_job_files                            = yes
 remove_job_temp_files                       = yes
 
-# Converting to fastq
-# Fastq converter config format 1 for reads stored in separate files for each end
-#  data_lane_rexex_N is a perl regex which stores the lane id in $1
-#  data_end_regex_N is a perl regex which stores the end, 1 or 2, in $1
-#  data_compress_regex_N is a perl regex which stores the compression extension in $1
-#  data_convert_N is the associated conversion utility that takes data at stdin and outputs fastq at stdout
-# Fastq converter config format 2 for reads stored in separate files for each end
-#  data_lane_regex_N is a perl regex which stores the lane id in $1
-#  data_compress_regex_N is a perl regex which stores the compression extension in $1
-#  data_end1_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 1 at stdout
-#  data_end2_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 2 at stdout
-
-data_lane_regex_1                           = ^(.+)_[12]_export\.txt.*$
-data_end_regex_1                            = ^.+_([12])_export\.txt.*$
-data_compress_regex_1                       = ^.+_[12]_export\.txt(.*)$
-data_converter_1                            = $(scripts_directory)/fq_all2std.pl export2std
-
-data_lane_regex_2                           = ^(.+)_[12]_concat_qseq\.txt.*$
-data_end_regex_2                            = ^.+_([12])_concat_qseq\.txt.*$
-data_compress_regex_2                       = ^.+_[12]_concat_qseq\.txt(.*)$
-data_converter_2                            = $(scripts_directory)/qseq2fastq.pl
-
-data_lane_regex_3                           = ^(.+)\.bam.*$
-data_compress_regex_3                       = ^.+\.bam(.*)$
-data_end1_converter_3                       = samtools view - | filter_sam_mate.pl 1 | sam_to_fastq.pl
-data_end2_converter_3                       = samtools view - | filter_sam_mate.pl 2 | sam_to_fastq.pl
-
-data_lane_regex_4                           = ^(.+).[12].fastq.*$
-data_end_regex_4                            = ^.+.([12]).fastq.*$
-data_compress_regex_4                       = ^.+.[12].fastq(.*)$
-data_converter_4                            = cat
 #end raw
 
-#end if
 
   </configfile>
   <configfile name="shscript">
@@ -602,7 +524,7 @@
 perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
 ## copy primary results to output datasets
 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
-if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
+## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi
 ## create html with links for output_dir
@@ -650,7 +572,7 @@
 
 If your fastq files have reads in different orders or include unpaired reads,  you can preprocess them with **FASTQ interlacer** to create a single interlaced fastq dataset with only the paired reads and input that to **FASTQ de-interlacer** to separate the reads into a left fastq and right fastq.
 
-DeFuse uses a Reference Dataset to search for gene fusions.  The Reference Dataset is generated from the following sources in DeFuse_Version_0.6_:
+DeFuse uses a Reference Dataset to search for gene fusions.  The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_:
     - genome_fasta from Ensembl 
     - gene_models from Ensembl 
     - repeats_filename from UCSC RepeatMasker rmsk.txt
@@ -658,7 +580,7 @@
     - est_alignments from UCSC intronEst.txt
     - unigene_fasta from NCBI
 
-.. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
+.. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
 
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