annotate defuse.xml @ 16:bdd93719cede draft

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author jjohnson
date Mon, 18 Dec 2017 09:31:31 -0500
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children c3167ccca38c
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1 <tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.2">
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2 <description>identify fusion transcripts</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <expand macro="defuse_requirement" />
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8 <expand macro="mapping_requirements" />
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9 <expand macro="r_requirements" />
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10 </requirements>
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c90022a13c7c DeFuse - Allow user to save the workspace, create an html file with links to the files in the workspace.
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11 <command interpreter="command"> /bin/bash $shscript </command>
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12 <inputs>
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13 <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.)"/>
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14 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
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15 <param name="library_name" type="text" value="unknown" label="library name" help="Value to put in the results library_name column">
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16 <validator type="length" min="1"/>
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17 </param>
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18 <conditional name="refGenomeSource">
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19 <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
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20 <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
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21 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
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22 </param>
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23 <when value="indexed">
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24 <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team">
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25 <options from_file="defuse_reference.loc">
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26 <column name="name" index="1"/>
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27 <column name="value" index="3"/>
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28 <filter type="sort_by" column="0" />
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29 <validator type="no_options" message="No indexes are available" />
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30 </options>
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31 </param>
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32 </when>
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33 <when value="history">
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34 <param name="config" type="data" format="defuse.conf" label="Defuse Config file" help=""/>
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35 </when> <!-- history -->
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36 </conditional> <!-- refGenomeSource -->
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37 <conditional name="defuse_param">
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38 <param name="settings" type="select" label="Defuse parameter settings" help="">
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39 <option value="preSet">Default settings</option>
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40 <option value="full">Full parameter list</option>
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41 </param>
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42 <when value="preSet" />
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43 <when value="full">
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44 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
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45 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
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46 <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)" />
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47 <param name="calculate_extra_annotations" type="select" label="Calculate extra annotations, fusion splice index and interrupted index" help="">
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48 <option value="">Use Default</option>
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49 <option value="no">no</option>
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50 <option value="yes">yes</option>
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51 </param>
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52 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
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53 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
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54 </param>
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55 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
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56 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
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57 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
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58 </param>
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59 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
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60 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
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61 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
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62 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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63 </param>
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64 <param name="multi_exon_transcripts_stats" type="select" label="Use multiple exon transcripts for stats calculations" help="should be enabled for very small libraries">
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65 <option value="no" select="true">no</option>
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66 <option value="yes">yes</option>
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67 </param>
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68 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
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69 <help>Position density when calculating covariance</help>
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70 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
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71 </param>
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72 <param name="max_paired_alignments" type="integer" value="10" optional="true" label="max_paired_alignments">
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73 <help>Maximum number of alignments for a read pair, Pairs with more alignments are filtered, default is 10</help>
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74 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="1" max="100"/>
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75 </param>
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76 <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
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77 <option value="">Use Default</option>
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78 <option value="no">no</option>
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79 <option value="yes">yes</option>
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80 </param>
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81 <!--
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82 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
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83 -->
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84 <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" />
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85 </when> <!-- full -->
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86 </conditional> <!-- defuse_param -->
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87 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"
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88 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run,
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89 but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
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90 <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
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91 <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
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92 </inputs>
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93 <stdio>
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94 <exit_code range="1:" level="fatal" description="Error Running Defuse" />
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95 </stdio>
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96 <outputs>
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97 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
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98 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
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99 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">
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100 <filter>keep_output == True</filter>
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101 </data>
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102 <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
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103 <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
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104 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
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105 <filter>do_get_reads == True</filter>
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106 </data>
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107 <data format="bam" name="fusions_bam" label="${tool.name} on ${on_string}: fusions.bam">
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108 <filter>breakpoints_bam == True</filter>
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109 </data>
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110 <!--
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111 expression_plot
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112 circos plot
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113 -->
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114 </outputs>
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115 <configfiles>
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116 <configfile name="defuse_config">
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117 #import re
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118 #set $ds = chr(36)
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119 #if $refGenomeSource.genomeSource == "history":
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120 #set config_file = $refGenomeSource.config.__str__
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121 #else
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122 #set config_file = $refGenomeSource.index.value
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123 #end if
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124 #set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$'
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125 #set fh = open($config_file)
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126 #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']
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127 #set kv = []
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128 #for $line in $fh:
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129 #set m = $re.match($pat,$line)
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130 #if $m and len($m.groups()) == 2:
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131 ## #echo $line
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132 #if $m.groups()[0] in keys:
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133 #set k = $m.groups()[0]
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134 #if k == 'dataset_directory' and $refGenomeSource.genomeSource == "indexed":
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135 ## The DataManager is conifgured to place the config file in the same directory as the defuse_data: dataset_directory
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136 #set v = $os.path.dirname($config_file)
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137 #else:
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138 #set v = $m.groups()[1]
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139 #end if
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140 #set kv = $kv + [[$k, $v]]
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141 #end if
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142 #end if
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143 #end for
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144 ## #echo $kv
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145 #set ref_dict = dict($kv)
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146 ## #echo $ref_dict
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147 ## include raw $refGenomeSource.config.__str__
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148 #
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149 # Configuration file for defuse
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150 #
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151 # At a minimum, change all values enclused by []
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152 #
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153
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154 # Directory where the defuse code was unpacked
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155 ## Default location in the tool/defuse directory
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156 # source_directory = ${__root_dir__}/tools/defuse
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157 source_directory = __DEFUSE_PATH__
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158
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159 # Directory where you want your dataset
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160 dataset_directory = #slurp
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161 #try
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162 $ref_dict['dataset_directory']
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163 #except
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164 /project/db/genomes/Hsapiens/hg19/defuse
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165 #end try
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166
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167 # Organism IDs
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168 ensembl_organism = #slurp
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169 #try
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170 $ref_dict['ensembl_organism']
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171 #except
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172 homo_sapiens
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173 #end try
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174
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175 ensembl_prefix = #slurp
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176 #try
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177 $ref_dict['ensembl_prefix']
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178 #except
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179 Homo_sapiens
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180 #end try
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181
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182 ensembl_version = #slurp
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183 #try
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184 $ref_dict['ensembl_version']
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185 #except
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186 71
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187 #end try
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188
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189 ensembl_genome_version = #slurp
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190 #try
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191 $ref_dict['ensembl_genome_version']
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192 #except
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193 GRCh37
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194 #end try
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195
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196 ucsc_genome_version = #slurp
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197 #try
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198 $ref_dict['ucsc_genome_version']
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199 #except
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200 hg19
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201 #end try
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202
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203 ncbi_organism = #slurp
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204 #try
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205 $ref_dict['ncbi_organism']
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206 #except
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207 Homo_sapiens
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208 #end try
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209
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210 ncbi_prefix = #slurp
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211 #try
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212 $ref_dict['ncbi_prefix']
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213 #except
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214 Hs
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215 #end try
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216
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217 # Input genome and gene models
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218 gene_models = #slurp
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219 #try
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220 $ref_dict['gene_models']
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221 #except
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222 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf
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223 #end try
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224 genome_fasta = #slurp
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225 #try
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226 $ref_dict['genome_fasta']
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227 #except
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228 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa
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229 #end try
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230
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231 # Repeat table from ucsc genome browser
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232 repeats_filename = #slurp
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233 #try
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234 $ref_dict['repeats_filename']
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235 #except
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236 \$(dataset_directory)/rmsk.txt
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237 #end try
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238
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239 # EST info downloaded from ucsc genome browser
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240 est_fasta = #slurp
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241 #try
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242 $ref_dict['est_fasta']
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243 #except
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244 \$(dataset_directory)/est.fa
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245 #end try
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246 est_alignments = #slurp
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247 #try
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248 $ref_dict['est_alignments']
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249 #except
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250 \$(dataset_directory)/intronEst.txt
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251 #end try
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252
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253 # Unigene clusters downloaded from ncbi
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254 unigene_fasta = #slurp
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255 #try
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256 $ref_dict['unigene_fasta']
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257 #except
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258 \$(dataset_directory)/\$(ncbi_prefix).seq.uniq
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259 #end try
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260
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261 # Paths to external tools
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262 bowtie_bin = __BOWTIE_BIN__
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263 bowtie_build_bin = __BOWTIE_BUILD_BIN__
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264 blat_bin = __BLAT_BIN__
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265 fatotwobit_bin = __FATOTWOBIT_BIN__
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266 gmap_bin = __GMAP_BIN__
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267 gmap_bin = __GMAP_BIN__
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268 gmap_setup_bin = __GMAP_SETUP_BIN__
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269 r_bin = __R_BIN__
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270 rscript_bin = __RSCRIPT_BIN__
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271
9
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272 # Directory where you want your dataset
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273 gmap_index_directory = #slurp
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274 #try
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275 $ref_dict['gmap_index_directory']
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276 #except
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277 #raw
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278 $(dataset_directory)/gmap
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279 #end raw
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280 #end try
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281
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282 #raw
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283 # Dataset files
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284 dataset_prefix = $(dataset_directory)/defuse
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285 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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286 exons_fasta = $(dataset_prefix).exons.fa
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287 cds_fasta = $(dataset_prefix).cds.fa
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288 cdna_regions = $(dataset_prefix).cdna.regions
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289 cdna_fasta = $(dataset_prefix).cdna.fa
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290 reference_fasta = $(dataset_prefix).reference.fa
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291 rrna_fasta = $(dataset_prefix).rrna.fa
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292 ig_gene_list = $(dataset_prefix).ig.gene.list
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293 repeats_regions = $(dataset_directory)/repeats.regions
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294 est_split_fasta1 = $(dataset_directory)/est.1.fa
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295 est_split_fasta2 = $(dataset_directory)/est.2.fa
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296 est_split_fasta3 = $(dataset_directory)/est.3.fa
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297 est_split_fasta4 = $(dataset_directory)/est.4.fa
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298 est_split_fasta5 = $(dataset_directory)/est.5.fa
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299 est_split_fasta6 = $(dataset_directory)/est.6.fa
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300 est_split_fasta7 = $(dataset_directory)/est.7.fa
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301 est_split_fasta8 = $(dataset_directory)/est.8.fa
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302 est_split_fasta9 = $(dataset_directory)/est.9.fa
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303
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304 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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305 prefilter1 = $(unigene_fasta)
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306
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307 # deFuse scripts and tools
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308 scripts_directory = $(source_directory)/scripts
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309 tools_directory = $(source_directory)/tools
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310 data_directory = $(source_directory)/data
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311 #end raw
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312
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313 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk
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314 samtools_bin = #slurp
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315 #try
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316 $ref_dict['samtools_bin']
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317 #except
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318 \$(source_directory)/external/samtools-0.1.8/samtools
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319 #end try
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320
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321 # Bowtie parameters
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322 bowtie_threads = #slurp
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323 #try
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324 $ref_dict['bowtie_threads']
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325 #except
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c90022a13c7c DeFuse - Allow user to save the workspace, create an html file with links to the files in the workspace.
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326 4
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327 #end try
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328 bowtie_quals = #slurp
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329 #try
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330 $ref_dict['bowtie_quals']
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331 #except
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332 --phred33-quals
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333 #end try
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334 bowtie_params = #slurp
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335 #try
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336 $ref_dict['bowtie_params']
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337 #except
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338 --chunkmbs 200
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339 #end try
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340 max_insert_size = #slurp
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341 #if $defuse_param.settings == "full" and $defuse_param.max_insert_size.__str__ != "":
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342 $defuse_param.max_insert_size
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343 #else
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344 #try
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345 $ref_dict['max_insert_size']
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346 #except
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347 500
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348 #end try
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349 #end if
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350
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351 # Parameters for building the dataset
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352 chromosomes = #slurp
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353 #try
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354 $ref_dict.chromosomes
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355 #except
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356 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
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357 #end try
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358 mt_chromosome = #slurp
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359 #try
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360 $ref_dict['mt_chromosome']
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361 #except
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362 MT
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363 #end try
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364 gene_sources = #slurp
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365 #try
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366 $ref_dict['gene_sources']
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367 #except
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368 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding
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369 #end try
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370 ig_gene_sources = #slurp
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371 #try
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372 $ref_dict['ig_gene_sources']
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373 #except
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374 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene
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375 #end try
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376 rrna_gene_sources = #slurp
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377 #try
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378 $ref_dict['rrna_gene_sources']
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379 #except
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380 Mt_rRNA,rRNA,rRNA_pseudogene
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381 #end try
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382
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383 # Blat sequences per job
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384 num_blat_sequences = #slurp
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385 #try
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386 $ref_dict['num_blat_sequences']
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387 #except
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388 10000
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389 #end try
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390
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391 # Minimum gene fusion range
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392 dna_concordant_length = #slurp
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393 #if $defuse_param.settings == "full" and $defuse_param.dna_concordant_length.__str__ != "":
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394 $defuse_param.dna_concordant_length
1
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395 #else
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396 #try
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397 $ref_dict['dna_concordant_length']
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398 #except
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399 2000
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400 #end try
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401 #end if
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402
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403 # Trim length for discordant reads (split reads are not trimmed)
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404 discord_read_trim = #slurp
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405 #if $defuse_param.settings == "full" and $defuse_param.discord_read_trim.__str__ != "":
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406 $defuse_param.discord_read_trim
1
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407 #else
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408 #try
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409 $ref_dict['discord_read_trim']
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410 #except
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411 50
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412 #end try
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413 #end if
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414 # Calculate extra annotations, fusion splice index and interrupted index
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415 calculate_extra_annotations = #slurp
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416 #if $defuse_param.settings == "full" and $defuse_param.calculate_extra_annotations.__str__ != "":
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417 $defuse_param.calculate_extra_annotations
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418 #else
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419 #try
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420 $ref_dict['calculate_extra_annotations']
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421 #except
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422 no
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423 #end try
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424 #end if
1
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425 # Filtering parameters
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426 clustering_precision = #slurp
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427 #if $defuse_param.settings == "full" and $defuse_param.clustering_precision.__str__ != ""
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428 $defuse_param.clustering_precision
1
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429 #else
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430 #try
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431 $ref_dict['clustering_precision']
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432 #except
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433 0.95
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434 #end try
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435 #end if
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436 span_count_threshold = #slurp
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437 #if $defuse_param.settings == "full" and $defuse_param.span_count_threshold.__str__ != ""
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438 $defuse_param.span_count_threshold
1
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439 #else
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440 #try
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441 $ref_dict['span_count_threshold']
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442 #except
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443 5
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444 #end try
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445 #end if
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446 percent_identity_threshold = #slurp
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447 #if $defuse_param.settings == "full" and $defuse_param.percent_identity_threshold.__str__ != ""
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448 $defuse_param.percent_identity_threshold
1
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449 #else
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450 #try
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451 $ref_dict['percent_identity_threshold']
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452 #except
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453 0.90
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454 #end try
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455 #end if
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456 split_min_anchor = #slurp
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457 #if $defuse_param.settings == "full" and $defuse_param.split_min_anchor.__str__ != ""
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458 $defuse_param.split_min_anchor
1
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459 #else
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460 #try
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461 $ref_dict['split_min_anchor']
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462 #except
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463 4
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464 #end try
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465 #end if
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466 splice_bias = #slurp
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467 #if $defuse_param.settings == "full" and $defuse_param.splice_bias.__str__ != ""
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468 $defuse_param.splice_bias
1
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469 #else
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470 #try
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471 $ref_dict['splice_bias']
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472 #except
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473 10
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474 #end try
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475 #end if
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476 denovo_assembly = #slurp
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477 #if $defuse_param.settings == "full" and $defuse_param.denovo_assembly.__str__ != ""
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478 $defuse_param.denovo_assembly
1
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479 #else
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480 #try
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481 $ref_dict['denovo_assembly']
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482 #except
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483 no
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484 #end try
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485 #end if
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486 probability_threshold = #slurp
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487 #if $defuse_param.settings == "full" and $defuse_param.probability_threshold.__str__ != ""
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488 $defuse_param.probability_threshold
1
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489 #else
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490 #try
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491 $ref_dict['probability_threshold']
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492 #except
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493 0.50
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494 #end try
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495 #end if
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496 positive_controls = \$(data_directory)/controls.txt
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497
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498 # Use multiple exon transcripts for stats calculations (yes/no)
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499 # should be enabled for very small libraries
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500 multi_exon_transcripts_stats = #slurp
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501 #if $defuse_param.settings == "full" and $defuse_param.multi_exon_transcripts_stats.__str__ != ""
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502 $defuse_param.multi_exon_transcripts_stats
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503 #else
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504 #try
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505 $ref_dict['multi_exon_transcripts_stats']
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506 #except
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507 no
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508 #end try
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509 #end if
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510
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511 # Position density when calculating covariance
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512 covariance_sampling_density = #slurp
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513 #if $defuse_param.settings == "full" and $defuse_param.covariance_sampling_density.__str__ != ""
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514 $defuse_param.covariance_sampling_density
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515 #else
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516 #try
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517 $ref_dict['covariance_sampling_density']
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518 #except
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519 0.01
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520 #end try
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521 #end if
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522
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523 # Maximum number of alignments for a read pair
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524 # Pairs with more alignments are filtered
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525 max_paired_alignments = #slurp
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526 #if $defuse_param.settings == "full" and $defuse_param.max_paired_alignments.__str__ != ""
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527 $defuse_param.max_paired_alignments
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528 #else
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529 #try
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530 $ref_dict['max_paired_alignments']
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531 #except
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532 10
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533 #end try
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534 #end if
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535
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536 # Number of reads for each job in split
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537 reads_per_job = #slurp
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538 #if $defuse_param.settings == "full" and $defuse_param.reads_per_job.__str__ != ""
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539 $defuse_param.reads_per_job
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540 #else
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541 #try
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542 $ref_dict['reads_per_job']
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543 #except
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544 1000000
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545 #end try
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546 #end if
1
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547
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548 #raw
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549 # If you have command line 'mail' and wish to be notified
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550 # mailto = andrew.mcpherson@gmail.com
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551
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552 # Remove temp files
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553 remove_job_files = yes
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554 remove_job_temp_files = yes
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555
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556 qsub_params = ""
1
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557
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558 #end raw
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559
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560
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561 </configfile>
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562 <configfile name="shscript">
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563 #!/bin/bash
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564 ## define some things for cheetah proccessing
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565 #set $ds = chr(36)
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566 #set $amp = chr(38)
3
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567 #set $gt = chr(62)
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568 #set $lt = chr(60)
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569 #set $echo_cmd = 'echo'
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570 ## Find the defuse.pl in the galaxy tool path
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571 #import Cheetah.FileUtils
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572 ## declare a bash function for converting a results tsv into html with links to the get_reads output files
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573 results2html() {
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574 rlts=${ds}1
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575 rslt_name=`basename ${ds}rlts`
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576 html=${ds}2
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577 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse '${ds}rslt_name'${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} ${ds}html
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578 echo '${lt}h2${gt}Defuse '${ds}rslt_name'${lt}/h2${gt}${lt}table${gt}' ${gt}${gt} ${ds}html
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579 if [ -z "${ds}3" ]
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580 then
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581 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");}\
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582 ${ds}1 ~ /[1-9][0-9]*/{printf("${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} ${ds}html
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583 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
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584 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html
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585 else
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586 export _EFP=${ds}3
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587 mkdir -p ${ds}_EFP
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588 awk '${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");}\
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589 ${ds}1 ~ /[1-9][0-9]*/{fn="cluster_"${ds}1"_reads.txt"; \
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590 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} ${ds}html
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591 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html
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592 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html
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593 for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`;
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594 do fn=cluster_${ds}{i}_reads.txt;
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595 pn=${ds}_EFP/${ds}fn;
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596 perl \${DEFUSE_PATH}/scripts/get_reads.pl -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn;
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597 done
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598 fi
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599 }
4
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600 ## substitute pathnames into config file
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601 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
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parents: 3
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602 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
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diff changeset
603 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
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parents: 3
diff changeset
604 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
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parents: 3
diff changeset
605 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
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diff changeset
606 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
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607 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
9
9f30de0ff090 Add gmap_setup_bin and gmap_index_directory to defuse.xml config file generation
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parents: 8
diff changeset
608 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
4
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609 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
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610 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
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611
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612
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613 ## copy config to output
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614 cp $defuse_config $config_txt
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615 ## make a data_dir and ln -s the input fastq
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616 mkdir -p data_dir
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617 ## ln -s "$left_pairendreads" data_dir/reads_1.fastq
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618 ## ln -s "$right_pairendreads" data_dir/reads_2.fastq
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619 cp "$left_pairendreads" data_dir/reads_1.fastq
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620 cp "$right_pairendreads" data_dir/reads_2.fastq
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621 ## ln to output_dir in from_work_dir
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622 #if $defuse_out.__str__ != 'None':
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623 mkdir -p $defuse_out.dataset.extra_files_path
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624 ln -s $defuse_out.dataset.extra_files_path output_dir
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625 #else
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626 mkdir -p output_dir
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627 #end if
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628 ## run defuse.pl
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629 perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS;
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630 exit_code_for_galaxy=\$?;
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631 ## copy primary results to output datasets
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632 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
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633 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
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634 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
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635 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi
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636 #if $breakpoints_bam:
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637 if [ -e output_dir/results.filtered.tsv ] ${amp}${amp} [ -e output_dir/breakpoints.genome.psl ]
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638 then
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639 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}
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640 psl2sam.pl breakpoints.genome.filtered.psl > breakpoints.genome.filtered.sam ${amp}${amp}
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641 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}
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642 samtools sort breakpoints.genome.filtered.bam breakpoints ${amp}${amp}
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643 ## samtools index breakpoints.bam
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644 cp breakpoints.bam $fusions_bam
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645 fi
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646 #end if
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647 ## create html with links for output_dir
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648 #if $defuse_out.__str__ != 'None':
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649 if [ -e $defuse_out ]
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650 then
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651 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out
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652 echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out
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653 pushd $defuse_out.dataset.extra_files_path
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654 for f in `find -L . -maxdepth 1 -type f`;
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655 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} $defuse_out;
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656 done
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657 popd
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658 echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out
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659 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} $defuse_out
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660 fi
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661 #end if
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662 ## run get_reads.pl on each cluster
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663 #if $fusion_reads.__str__ != 'None':
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664 if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ]
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665 then
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666 mkdir -p $fusion_reads.dataset.extra_files_path
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667 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path
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668 fi
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669 #end if
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670 (exit \$exit_code_for_galaxy)
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671 </configfile>
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672 </configfiles>
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673
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674 <tests>
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675 </tests>
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676 <help>
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677 **DeFuse**
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678
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679 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.
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680
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681 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
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682
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683 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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684
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685 ------
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686
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687 **Inputs**
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688
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689 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**).
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690
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691 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.
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692
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693 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_:
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694 - genome_fasta from Ensembl
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695 - gene_models from Ensembl
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696 - repeats_filename from UCSC RepeatMasker rmsk.txt
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697 - est_fasta from UCSC
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698 - est_alignments from UCSC intronEst.txt
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699 - unigene_fasta from NCBI
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700
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701 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2
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702
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703 ------
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704
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705 **Outputs**
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706
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707 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.
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708
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709 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.
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710
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711 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order):
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712
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713 - **Identification**
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714 - cluster_id : random identifier assigned to each prediction
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715 - library_name : library name given on the command line of defuse
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716 - gene1 : ensembl id of gene 1
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717 - gene2 : ensembl id of gene 2
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718 - gene_name1 : name of gene 1
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719 - gene_name2 : name of gene 2
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720 - **Evidence**
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721 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable
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722 - concordant_ratio : proportion of spanning reads considered concordant by blat
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723 - denovo_min_count : minimum kmer count across denovo assembled sequence
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724 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly
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725 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive
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726 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1
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727 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2
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728 - min_map_count : minimum of the number of genomic mappings for each spanning read
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729 - max_map_count : maximum of the number of genomic mappings for each spanning read
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730 - mean_map_count : average of the number of genomic mappings for each spanning read
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731 - num_multi_map : number of spanning reads that map to more than one genomic location
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732 - span_count : number of spanning reads supporting the fusion
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733 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage
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734 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage
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735 - span_coverage_min : minimum of span_coverage1 and span_coverage2
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736 - span_coverage_max : maximum of span_coverage1 and span_coverage2
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737 - splitr_count : number of split reads supporting the prediction
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738 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive
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739 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive
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740 - splitr_sequence : fusion sequence predicted by split reads
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741 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive
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742 - **Annotation**
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743 - adjacent : fusion between adjacent genes
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744 - altsplice : fusion likely the product of alternative splicing between adjacent genes
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745 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1
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746 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2
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747 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2
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748 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2
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749 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands
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750 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna
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751 - deletion : fusion produced by a genomic deletion
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752 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est
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753 - eversion : fusion produced by a genomic eversion
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754 - exonboundaries : fusion splice at exon boundaries
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755 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons
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756 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons
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757 - gene_chromosome1 : chromosome of gene 1
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758 - gene_chromosome2 : chromosome of gene 2
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759 - gene_end1 : end position for gene 1
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760 - gene_end2 : end position for gene 2
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761 - gene_location1 : location of breakpoint in gene 1
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762 - gene_location2 : location of breakpoint in gene 2
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763 - gene_start1 : start of gene 1
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764 - gene_start2 : start of gene 2
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765 - gene_strand1 : strand of gene 1
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766 - gene_strand2 : strand of gene 2
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767 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome
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768 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint
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769 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint
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770 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
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771 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream
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772 - interchromosomal : fusion produced by an interchromosomal translocation
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773 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1
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774 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2
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775 - inversion : fusion produced by genomic inversion
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776 - orf : fusion combines genes in a way that preserves a reading frame
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777 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt)
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778 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement
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779 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region
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780 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region
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781 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2
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782 - splice_score : number of nucleotides similar to GTAG at fusion splice
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783 - num_splice_variants : number of potential splice variants for this gene pair
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784 - 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
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785 - 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
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786
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787
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788 **Example**
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789
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790 results.tsv::
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791
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792 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
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793 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 -
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794 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 - -
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795
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796 </help>
11
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797 <expand macro="citations"/>
1
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798 </tool>