--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/defuse.xml	Mon May 20 15:25:03 2019 -0400
@@ -0,0 +1,701 @@
+<tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.1">
+    <description>identify fusion transcripts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="defuse_requirement" />
+    </requirements>
+  <command detect_errors="default"><![CDATA[
+    #if $defuse_out.__str__ != 'None':
+        ## ln to output_dir in from_work_dir
+        mkdir -p $defuse_out.files_path &&
+        ln -s $defuse_out.files_path  output_dir &&
+    #else
+      mkdir -p output_dir &&
+    #end if
+    ## Put executable paths in config file
+    $__tool_directory__/config_sub.sh $defuse_config output_dir/defuse.cfg &&
+    ## copy config to output
+    cp output_dir/defuse.cfg $config_txt &&
+    ## make a data_dir  and ln -s the input fastq
+    mkdir -p data_dir &&
+    ln -s "$left_pairendreads" data_dir/reads_1.fastq &&
+    ln -s "$right_pairendreads" data_dir/reads_2.fastq &&
+    ## run 
+    DATASET_DIRECTORY=`grep '^dataset_directory' output_dir/defuse.cfg | awk '{print \$NF}'` &&
+    defuse_run.pl --name "$library_name" --config output_dir/defuse.cfg --dataset \$DATASET_DIRECTORY -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p \$GALAXY_SLOTS &&
+    grep -v cluster_id  output_dir/results.filtered.tsv | awk '{print $1}' > cluster_id_list && 
+    get_fusion_fastq.pl --list cluster_id_list --output output_dir --fastq1 results.fusions_1.fq --fastq2 results.fusions_2.fq && 
+    cp output_dir/results.* .  &&
+    cp `find -L output_dir -name defuse.log` $defuse_log 
+    #if $defuse_out.__str__ != 'None':
+        && $__tool_directory__/make_html.sh $defuse_out $defuse_out.files_path
+    #end if
+  ]]></command>
+ <configfiles>
+  <configfile name="defuse_config">
+#import re
+#if $refGenomeSource.genomeSource == "history":
+#set config_file = $refGenomeSource.config.__str__
+#else 
+#set config_file = $refGenomeSource.index.value
+#end if
+#set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$'
+#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:
+  #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
+#
+# At a minimum, change all values enclused by []
+#
+
+# Directory where the defuse code was unpacked
+## Default location in the tool/defuse directory  
+# source_directory = ${__root_dir__}/tools/defuse
+source_directory = __DEFUSE_PATH__
+
+# Directory where you want your dataset
+dataset_directory = #slurp
+#try
+$ref_dict['dataset_directory']
+#except
+/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)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf
+#end try
+genome_fasta = #slurp
+#try
+$ref_dict['genome_fasta']
+#except
+\$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa
+#end try
+
+# Repeat table from ucsc genome browser
+repeats_filename = #slurp
+#try
+$ref_dict['repeats_filename']
+#except
+\$(dataset_directory)/rmsk.txt
+#end try
+
+# EST info downloaded from ucsc genome browser
+est_fasta = #slurp
+#try
+$ref_dict['est_fasta']
+#except
+\$(dataset_directory)/est.fa
+#end try
+est_alignments = #slurp
+#try
+$ref_dict['est_alignments']
+#except
+\$(dataset_directory)/intronEst.txt
+#end try
+
+# Unigene clusters downloaded from ncbi
+unigene_fasta = #slurp
+#try
+$ref_dict['unigene_fasta']
+#except
+\$(dataset_directory)/\$(ncbi_prefix).seq.uniq
+#end try
+
+# Paths to external tools
+bowtie_bin = __BOWTIE_BIN__
+bowtie_build_bin = __BOWTIE_BUILD_BIN__
+blat_bin = __BLAT_BIN__
+fatotwobit_bin = __FATOTWOBIT_BIN__
+gmap_bin = __GMAP_BIN__
+gmap_bin = __GMAP_BIN__
+gmap_setup_bin = __GMAP_SETUP_BIN__
+r_bin = __R_BIN__
+rscript_bin = __RSCRIPT_BIN__
+
+# Directory where you want your dataset
+gmap_index_directory = #slurp
+#try
+$ref_dict['gmap_index_directory']
+#except
+#raw
+$(dataset_directory)/gmap
+#end raw
+#end try
+
+#raw
+# Dataset files
+dataset_prefix       = $(dataset_directory)/defuse
+chromosome_prefix    = $(dataset_prefix).dna.chromosomes
+exons_fasta          = $(dataset_prefix).exons.fa
+cds_fasta            = $(dataset_prefix).cds.fa
+cdna_regions         = $(dataset_prefix).cdna.regions
+cdna_fasta           = $(dataset_prefix).cdna.fa
+reference_fasta      = $(dataset_prefix).reference.fa
+rrna_fasta           = $(dataset_prefix).rrna.fa
+ig_gene_list         = $(dataset_prefix).ig.gene.list
+repeats_regions      = $(dataset_directory)/repeats.regions
+est_split_fasta1     = $(dataset_directory)/est.1.fa
+est_split_fasta2     = $(dataset_directory)/est.2.fa
+est_split_fasta3     = $(dataset_directory)/est.3.fa
+est_split_fasta4     = $(dataset_directory)/est.4.fa
+est_split_fasta5     = $(dataset_directory)/est.5.fa
+est_split_fasta6     = $(dataset_directory)/est.6.fa
+est_split_fasta7     = $(dataset_directory)/est.7.fa
+est_split_fasta8     = $(dataset_directory)/est.8.fa
+est_split_fasta9     = $(dataset_directory)/est.9.fa
+
+# Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
+prefilter1           = $(unigene_fasta)
+
+# deFuse scripts and tools
+scripts_directory    = $(source_directory)/scripts
+tools_directory      = $(source_directory)/tools
+data_directory       = $(source_directory)/data
+#end raw
+
+# Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk
+samtools_bin = #slurp 
+#try
+$ref_dict['samtools_bin']
+#except
+\$(source_directory)/external/samtools-0.1.8/samtools
+#end try
+
+# Bowtie parameters
+bowtie_threads = #slurp
+#try
+$ref_dict['bowtie_threads']
+#except
+4
+#end try
+bowtie_quals = #slurp
+#try
+$ref_dict['bowtie_quals']
+#except
+--phred33-quals
+#end try
+bowtie_params = #slurp
+#try
+$ref_dict['bowtie_params']
+#except
+--chunkmbs 200
+#end try
+max_insert_size = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.max_insert_size.__str__ != "":
+$defuse_param.max_insert_size
+#else
+#try
+$ref_dict['max_insert_size']
+#except
+500
+#end try
+#end if
+
+# Parameters for building the dataset
+chromosomes = #slurp
+#try 
+$ref_dict.chromosomes
+#except
+1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
+#end try
+mt_chromosome = #slurp
+#try 
+$ref_dict['mt_chromosome']
+#except
+MT
+#end try
+gene_sources = #slurp
+#try 
+$ref_dict['gene_sources']
+#except
+IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding
+#end try
+ig_gene_sources = #slurp
+#try 
+$ref_dict['ig_gene_sources']
+#except
+IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene
+#end try
+rrna_gene_sources = #slurp
+#try 
+$ref_dict['rrna_gene_sources']
+#except
+Mt_rRNA,rRNA,rRNA_pseudogene
+#end try
+
+# Blat sequences per job
+num_blat_sequences = #slurp
+#try
+$ref_dict['num_blat_sequences']
+#except
+10000
+#end try
+
+# Minimum gene fusion range
+dna_concordant_length = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.dna_concordant_length.__str__ != "":
+$defuse_param.dna_concordant_length
+#else
+#try
+$ref_dict['dna_concordant_length']
+#except
+2000
+#end try
+#end if
+
+# Trim length for discordant reads (split reads are not trimmed)
+discord_read_trim = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.discord_read_trim.__str__ != "":
+$defuse_param.discord_read_trim
+#else
+#try
+$ref_dict['discord_read_trim']
+#except
+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 $defuse_param.settings == "full" and $defuse_param.clustering_precision.__str__ != ""
+$defuse_param.clustering_precision
+#else
+#try
+$ref_dict['clustering_precision']
+#except
+0.95
+#end try
+#end if
+span_count_threshold = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.span_count_threshold.__str__ != ""
+$defuse_param.span_count_threshold
+#else
+#try
+$ref_dict['span_count_threshold']
+#except
+5
+#end try
+#end if
+percent_identity_threshold = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.percent_identity_threshold.__str__ != ""
+$defuse_param.percent_identity_threshold
+#else
+#try
+$ref_dict['percent_identity_threshold']
+#except
+0.90
+#end try
+#end if
+split_min_anchor = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.split_min_anchor.__str__ != ""
+$defuse_param.split_min_anchor
+#else
+#try
+$ref_dict['split_min_anchor']
+#except
+4
+#end try
+#end if
+splice_bias = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.splice_bias.__str__ != ""
+$defuse_param.splice_bias
+#else
+#try
+$ref_dict['splice_bias']
+#except
+10
+#end try
+#end if
+denovo_assembly = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.denovo_assembly.__str__ != ""
+$defuse_param.denovo_assembly
+#else
+#try
+$ref_dict['denovo_assembly']
+#except
+no
+#end try
+#end if
+probability_threshold = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.probability_threshold.__str__ != ""
+$defuse_param.probability_threshold
+#else
+#try
+$ref_dict['probability_threshold']
+#except
+0.50
+#end try
+#end if
+positive_controls                           = \$(data_directory)/controls.txt
+
+# Use multiple exon transcripts for stats calculations (yes/no)
+# should be enabled for very small libraries
+multi_exon_transcripts_stats = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.multi_exon_transcripts_stats.__str__ != ""
+$defuse_param.multi_exon_transcripts_stats
+#else
+#try
+$ref_dict['multi_exon_transcripts_stats']
+#except
+no
+#end try
+#end if
+
+# Position density when calculating covariance
+covariance_sampling_density = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.covariance_sampling_density.__str__ != ""
+$defuse_param.covariance_sampling_density
+#else
+#try
+$ref_dict['covariance_sampling_density']
+#except
+0.01
+#end try
+#end if
+
+# Maximum number of alignments for a read pair
+# Pairs with more alignments are filtered
+max_paired_alignments = #slurp
+#if $defuse_param.settings == "full" and $defuse_param.max_paired_alignments.__str__ != ""
+$defuse_param.max_paired_alignments
+#else
+#try
+$ref_dict['max_paired_alignments']
+#except
+10
+#end try
+#end if
+
+# Number of reads for each job in split
+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
+# mailto                                      = andrew.mcpherson@gmail.com
+
+# Remove temp files
+remove_job_files                            = yes
+remove_job_temp_files                       = yes
+
+qsub_params                                 = ""
+
+#end raw
+
+  </configfile>
+ </configfiles>
+ <inputs>
+  <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"/>
+  <param name="library_name" type="text" value="unknown" label="library name" help="Value to put in the results library_name column">
+    <validator type="length" min="1"/>
+  </param>
+  <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>
+    <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="3"/>
+          <filter type="sort_by" column="0" />
+          <validator type="no_options" message="No indexes are available" />
+        </options>
+      </param>
+    </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="multi_exon_transcripts_stats" type="select" label="Use multiple exon transcripts for stats calculations" help="should be enabled for very small libraries">
+        <option value="no" selected="true">no</option>
+        <option value="yes">yes</option>
+      </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="max_paired_alignments" type="integer" value="10" optional="true" label="max_paired_alignments">
+        <help>Maximum number of alignments for a read pair, Pairs with more alignments are filtered, default is 10</help>
+        <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="1" max="100"/>
+      </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."/>
+ </inputs>
+ <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 ${on_string}: defuse.log" />
+  <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">
+    <filter>keep_output == True</filter>
+  </data>
+  <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" from_work_dir="results.classify.tsv"/>
+  <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" from_work_dir="results.filtered.tsv"/>
+  <data format="fastqsanger" name="results_fusions1_fq" label="${tool.name} on ${on_string}: fusions_1.fq" from_work_dir="results.fusions_1.fq" />
+  <data format="fastqsanger" name="results_fusions2_fq" label="${tool.name} on ${on_string}: fusions_2.fq" from_work_dir="results.fusions_2.fq" />
+  <!--
+   expression_plot
+   circos plot
+  -->
+ </outputs>
+
+ <tests>
+ </tests>
+ <help>
+**DeFuse**
+
+DeFuse_ is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion.  
+
+Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
+
+.. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
+
+------
+
+**Inputs**
+
+DeFuse requires 2 fastq files for paried reads, one with the left mate of the paired reads, and a second fastq with the the right mate of the paired reads (**with reads in the same order as in the first fastq dataset**).   
+
+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_0.4_:
+    - genome_fasta from Ensembl 
+    - gene_models from Ensembl 
+    - repeats_filename from UCSC RepeatMasker rmsk.txt
+    - est_fasta from UCSC
+    - est_alignments from UCSC intronEst.txt
+    - unigene_fasta from NCBI
+
+.. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
+
+------
+
+**Outputs**
+
+The galaxy history will contain 5 outputs: the config.txt file that provides DeFuse with its parameters,  the defuse.log which details what DeFuse has done and can be useful in determining any errors, and the 3 results files that defuse generates.  
+
+DeFuse generates 3 results files: results.txt, results.filtered.txt, and results.classify.txt. All three files have the same format, though results.classify.txt has a probability column from the application of the classifier to results.txt, and results.filtered.txt has been filtered according to the threshold probability as set in config.txt. 
+
+The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order):
+
+ - **Identification**
+    - cluster_id : random identifier assigned to each prediction
+    - library_name : library name given on the command line of defuse
+    - gene1 : ensembl id of gene 1
+    - gene2 : ensembl id of gene 2
+    - gene_name1 : name of gene 1
+    - gene_name2 : name of gene 2
+ - **Evidence**
+    - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable
+    - concordant_ratio : proportion of spanning reads considered concordant by blat
+    - denovo_min_count : minimum kmer count across denovo assembled sequence
+    - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly
+    - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive
+    - gene_align_strand1 : alignment strand for spanning read alignments to gene 1
+    - gene_align_strand2 : alignment strand for spanning read alignments to gene 2
+    - min_map_count : minimum of the number of genomic mappings for each spanning read
+    - max_map_count : maximum of the number of genomic mappings for each spanning read
+    - mean_map_count : average of the number of genomic mappings for each spanning read
+    - num_multi_map : number of spanning reads that map to more than one genomic location
+    - span_count : number of spanning reads supporting the fusion
+    - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage
+    - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage
+    - span_coverage_min : minimum of span_coverage1 and span_coverage2
+    - span_coverage_max : maximum of span_coverage1 and span_coverage2
+    - splitr_count : number of split reads supporting the prediction
+    - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive
+    - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive
+    - splitr_sequence : fusion sequence predicted by split reads
+    - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive
+ - **Annotation**
+    - adjacent : fusion between adjacent genes
+    - altsplice : fusion likely the product of alternative splicing between adjacent genes
+    - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1
+    - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2
+    - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2
+    - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2
+    - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands
+    - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna
+    - deletion : fusion produced by a genomic deletion
+    - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est
+    - eversion : fusion produced by a genomic eversion
+    - exonboundaries : fusion splice at exon boundaries
+    - expression1 : expression of gene 1 as number of concordant pairs aligned to exons
+    - expression2 : expression of gene 2 as number of concordant pairs aligned to exons
+    - gene_chromosome1 : chromosome of gene 1
+    - gene_chromosome2 : chromosome of gene 2
+    - gene_end1 : end position for gene 1
+    - gene_end2 : end position for gene 2
+    - gene_location1 : location of breakpoint in gene 1
+    - gene_location2 : location of breakpoint in gene 2
+    - gene_start1 : start of gene 1
+    - gene_start2 : start of gene 2
+    - gene_strand1 : strand of gene 1
+    - gene_strand2 : strand of gene 2
+    - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome
+    - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint
+    - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint
+    - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
+    - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
+    - interchromosomal : fusion produced by an interchromosomal translocation
+    - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1
+    - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2
+    - inversion : fusion produced by genomic inversion
+    - orf : fusion combines genes in a way that preserves a reading frame
+    - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt)
+    - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement
+    - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region
+    - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region
+    - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2
+    - splice_score : number of nucleotides similar to GTAG at fusion splice
+    - num_splice_variants : number of potential splice variants for this gene pair
+    - splicing_index1 : number of concordant pairs in gene 1 spanning the fusion splice / breakpoint, divided by number of spanning reads supporting the fusion with gene 2
+    - splicing_index2 : number of concordant pairs in gene 2 spanning the fusion splice / breakpoint, divided by number of spanning reads supporting the fusion with gene 1
+
+
+**Example**
+
+results.tsv::
+
+  cluster_id	splitr_sequence	splitr_count	splitr_span_pvalue	splitr_pos_pvalue	splitr_min_pvalue	adjacent	altsplice	break_adj_entropy1	break_adj_entropy2	break_adj_entropy_min	break_predict	breakpoint_homology	breakseqs_estislands_percident	cdna_breakseqs_percident	concordant_ratio	deletion	est_breakseqs_percident	eversion	exonboundaries	expression1	expression2	gene1	gene2	gene_align_strand1	gene_align_strand2	gene_chromosome1	gene_chromosome2	gene_end1	gene_end2	gene_location1	gene_location2	gene_name1	gene_name2	gene_start1	gene_start2	gene_strand1	gene_strand2	genome_breakseqs_percident	genomic_break_pos1	genomic_break_pos2	genomic_strand1	genomic_strand2	interchromosomal	interrupted_index1	interrupted_index2	inversion	library_name	max_map_count	max_repeat_proportion	mean_map_count	min_map_count	num_multi_map	num_splice_variants	orf	read_through	repeat_proportion1	repeat_proportion2	span_count	span_coverage1	span_coverage2	span_coverage_max	span_coverage_min	splice_score	splicing_index1	splicing_index2	
+  1169	GCTTACTGTATGCCAGGCCCCAGAGGGGCAACCACCCTCTAAAGAGAGCGGCTCCTGCCTCCCAGAAAGCTCACAGACTGTGGGAGGGAAACAGGCAGCAGGTGAAGATGCCAAATGCCAGGATATCTGCCCTGTCCTTGCTTGATGCAGCTGCTGGCTCCCACGTTCTCCCCAGAATCCCCTCACACTCCTGCTGTTTTCTCTGCAGGTTGGCAGAGCCCCATGAGGGCAGGGCAGCCACTTTGTTCTTGGGCGGCAAACCTCCCTGGGCGGCACGGAAACCACGGTGAGAAGGGGGCAGGTCGGGCACGTGCAGGGACCACGCTGCAGG|TGTACCCAACAGCTCCGAAGAGACAGCGACCATCGAGAACGGGCCATGATGACGATGGCGGTTTTGTCGAAAAGAAAAGGGGGAAATGTGGGGAAAAGCAAGAGAGATCAGATTGTTACTGTGTCTGTGTAGAAAGAAGTAGACATGGGAGACTCCATTTTGTTCTGTACTAAGAAAAATTCTTCTGCCTTGAGATTCGGTGACCCCACCCCCAACCCCGTGCTCTCTGAAACATGTGCTGTGTCCACTCAGGGTTGAATGGATTAAGGGCGGTGCGAGACGTGCTTT	2	0.000436307890680442	0.110748295953850	0.0880671602973091	N	Y	3.19872427442695	3.48337348351473	3.19872427442695	splitr	0	0	0	0	Y	0	N	N	0	0	ENSG00000105549	ENSG00000213753	+	-	19	19	376013	59111168	intron	upstream	THEG	AC016629.2	361750	59084870	-	+	0	375099	386594	+	-	N	8.34107429512245	-	N	output_dir	82	0.677852348993289	40.6666666666667	1	11	1	N	N	0.361271676300578	0.677852348993289	12	0.758602776578432	0.569678713445872	0.758602776578432	0.569678713445872	2	0.416666666666667	-	
+  3596	TGGGGGTTGAGGCTTCTGTTCCCAGGTTCCATGACCTCAGAGGTGGCTGGTGAGGTTATGACCTTTGCCCTCCAGCCCTGGCTTAAAACCTCAGCCCTAGGACCTGGTTAAAGGAAGGGGAGATGGAGCTTTGCCCCGACCCCCCCCCGTTCCCCTCACCTGTCAGCCCGAGCTGGGCCAGGGCCCCTAGGTGGGGAACTGGGCCGGGGGGCGGGCACAAGCGGAGGTGGTGCCCCCAAAAGGGCTCCCGGTGGGGTCTTGCTGAGAAGGTGAGGGGTTCCCGGGGCCGCAGCAGGTGGTGGTGGAGGAGCCAAGCGGCTGTAGAGCAAGGGGTGAGCAGGTTCCAGACCGTAGAGGCGGGCAGCGGCCACGGCCCCGGGTCCAGTTAGCTCCTCACCCGCCTCATAGAAGCGGGGTGGCCTTGCCAGGCGTGGGGGTGCTGCC|TTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCAGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGCCCCCCGGCCGGGGCCGGAGAGGGGCTGACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCGCGAAGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTAGACATGCATGGCTTAATCTTTGAGACAAGCATATGCTACTGGCAGG	250	7.00711162298275e-72	0.00912124762512338	0.00684237452309549	N	N	3.31745197152461	3.47233119514066	3.31745197152461	splitr	7	0.0157657657657656	0	0	N	0.0135135135135136	N	N	0	0	ENSG00000156860	ENSG00000212932	-	+	16	21	30682131	48111157	coding	upstream	FBRS	RPL23AP4	30670289	48110676	+	+	0.0157657657657656	30680678	9827473	-	+	Y	-	-	N	output_dir	2	1	1.11111111111111	1	1	1	N	N	0	1	9	0.325530693397641	0.296465452915709	0.325530693397641	0.296465452915709	2	-	-	
+
+ </help>
+    <expand macro="citations"/>
+</tool>