<tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.2">
    <description>identify fusion transcripts</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <expand macro="defuse_requirement" />
        <expand macro="mapping_requirements" />
        <expand macro="r_requirements" />
    </requirements>
  <command interpreter="command"> /bin/bash $shscript </command>
 <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" select="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."/>
  <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
  <param name="do_get_reads" type="boolean" checked="false" 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 ${on_string}: defuse.log" />
  <data format="html" name="defuse_out" label="${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 ${on_string}: results.classify.tsv" />
  <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
  <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
    <filter>do_get_reads == True</filter>
  </data>
  <data format="bam" name="fusions_bam" label="${tool.name} on ${on_string}: fusions.bam">
    <filter>breakpoints_bam == True</filter>
  </data>
  <!--
   expression_plot
   circos plot
  -->
 </outputs>
 <configfiles>
  <configfile name="defuse_config">
#import re
#set $ds = chr(36)
#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>
  <configfile name="shscript">
#!/bin/bash
## define some things for cheetah proccessing
#set $ds = chr(36)
#set $amp = chr(38)
#set $gt = chr(62)
#set $lt = chr(60)
#set $echo_cmd = 'echo'
## Find the defuse.pl in the galaxy tool path
#import Cheetah.FileUtils
## declare a bash function for converting a results tsv into html with links to the get_reads output files
results2html() {
  rlts=${ds}1
  rslt_name=`basename ${ds}rlts`
  html=${ds}2
  echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse '${ds}rslt_name'${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt}  ${ds}html
  echo '${lt}h2${gt}Defuse '${ds}rslt_name'${lt}/h2${gt}${lt}table${gt}' ${gt}${gt}  ${ds}html
  if [ -z "${ds}3" ]  
  then
    awk '${ds}1 ~ /cluster_id/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}th${gt}%s${lt}/th${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}\
         ${ds}1 ~ /[1-9][0-9]*/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}td${gt}%s${lt}/td${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}' ${ds}rlts ${gt}${gt} ${ds}html
    echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
    echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt}  ${ds}html
  else
    export _EFP=${ds}3
    mkdir -p ${ds}_EFP
    awk '${ds}1 ~ /cluster_id/{printf("${lt}tr${gt}");for (i = 1; i ${lt}= NF; i++) {printf("${lt}th${gt}%s${lt}/th${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}\
         ${ds}1 ~ /[1-9][0-9]*/{fn="cluster_"${ds}1"_reads.txt"; \
          printf("${lt}tr${gt}${lt}td${gt}${lt}a href=\"%s\"${gt}%s${lt}/a${gt}${lt}/td${gt}",fn, ${ds}1);for (i = 2; i ${lt}= NF; i++) {printf("${lt}td${gt}%s${lt}/td${gt}", ${ds}i);}; printf("${lt}/tr${gt}\n");}' ${ds}rlts ${gt}${gt} ${ds}html
    echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
    echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt}  ${ds}html
    for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`;
      do fn=cluster_${ds}{i}_reads.txt;
      pn=${ds}_EFP/${ds}fn;
      perl \${DEFUSE_PATH}/scripts/get_reads.pl -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn;
    done
  fi
}
## substitute pathnames into config file
if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi


## copy config to output
cp $defuse_config $config_txt
## make a data_dir  and ln -s the input fastq
mkdir -p data_dir
## ln -s "$left_pairendreads" data_dir/reads_1.fastq
## ln -s "$right_pairendreads" data_dir/reads_2.fastq
cp "$left_pairendreads" data_dir/reads_1.fastq
cp "$right_pairendreads" data_dir/reads_2.fastq
## ln to output_dir in from_work_dir
#if $defuse_out.__str__ != 'None':
mkdir -p $defuse_out.dataset.extra_files_path
ln -s $defuse_out.dataset.extra_files_path  output_dir
#else
mkdir -p output_dir
#end if
## run defuse.pl
perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p \$GALAXY_SLOTS;
exit_code_for_galaxy=\$?;
## 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.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
#if $breakpoints_bam:
if [ -e output_dir/results.filtered.tsv ] ${amp}${amp}  [ -e output_dir/breakpoints.genome.psl ]
then
  awk "\\$10 ~ /^(`awk '\\$1 ~ /[0-9]+/{print \\$1}' output_dir/results.filtered.tsv | tr '\n' '|'`)\\$/{print \\$0}" output_dir/breakpoints.genome.psl > breakpoints.genome.filtered.psl ${amp}${amp}
  psl2sam.pl breakpoints.genome.filtered.psl > breakpoints.genome.filtered.sam ${amp}${amp}
  samtools view -b -T /panfs/roc/rissdb/galaxy/genomes/NCBIM37/defuse/defuse.reference.fa -o breakpoints.genome.filtered.bam breakpoints.genome.filtered.sam ${amp}${amp}
  samtools sort breakpoints.genome.filtered.bam breakpoints ${amp}${amp}
  ## samtools index breakpoints.bam
  cp breakpoints.bam $fusions_bam
fi
#end if
## create html with links for output_dir
#if $defuse_out.__str__ != 'None':
if [ -e $defuse_out ]
then
  echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out
  echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt}  $defuse_out
  pushd $defuse_out.dataset.extra_files_path
  for f in `find -L . -maxdepth 1 -type f`; 
   do fn=`basename ${ds}f`; echo '${lt}li${gt}${lt}a href="'${ds}fn'"${gt}'${ds}fn'${lt}/a${gt}${lt}/li${gt}' ${gt}${gt}  $defuse_out; 
  done
  popd
  echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out
  echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt}  $defuse_out
fi
#end if
## run get_reads.pl on each cluster
#if $fusion_reads.__str__ != 'None':
if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ] 
then
  mkdir -p $fusion_reads.dataset.extra_files_path
  results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path
fi
#end if
(exit \$exit_code_for_galaxy)
  </configfile>
 </configfiles>

 <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>