Mercurial > repos > jjohnson > defuse
annotate defuse.xml @ 23:e8fc5de0578b
defuse.xml fix unigene_fasta path to use ncbi_prefix
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 07 Aug 2013 11:54:05 -0500 |
| parents | 68494d6aabeb |
| children | 2ecf82136986 |
| rev | line source |
|---|---|
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1 <tool id="defuse" name="DeFuse" version="1.6.1"> |
| 0 | 2 <description>identify fusion transcripts</description> |
| 3 <requirements> | |
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4 <requirement type="package" version="0.6.1">defuse</requirement> |
| 6 | 5 <requirement type="package" version="0.1.18">samtools</requirement> |
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6 <requirement type="package" version="1.0.0">bowtie</requirement> |
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7 <requirement type="package" version="2013-05-09">gmap</requirement> |
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8 <requirement type="package" version="latest">kent</requirement> |
| 0 | 9 </requirements> |
| 10 <command interpreter="command"> /bin/bash $shscript </command> | |
| 11 <inputs> | |
| 12 <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.)"/> | |
| 13 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/> | |
| 14 <conditional name="refGenomeSource"> | |
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15 <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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16 <option value="indexed">Use a built-in DeFuse Reference Dataset</option> |
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17 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option> |
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18 </param> |
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19 <when value="indexed"> |
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20 <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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21 <options from_file="defuse_reference.loc"> |
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22 <column name="name" index="1"/> |
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23 <column name="value" index="3"/> |
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24 <filter type="sort_by" column="0" /> |
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25 <validator type="no_options" message="No indexes are available" /> |
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26 </options> |
| 0 | 27 </param> |
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28 </when> |
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29 <when value="history"> |
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30 <param name="config" type="data" format="defuse.conf" label="Defuse Config file" help=""/> |
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31 </when> <!-- history --> |
| 0 | 32 </conditional> <!-- refGenomeSource --> |
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33 <conditional name="defuse_param"> |
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34 <param name="settings" type="select" label="Defuse parameter settings" help=""> |
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35 <option value="preSet">Default settings</option> |
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36 <option value="full">Full parameter list</option> |
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37 </param> |
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38 <when value="preSet" /> |
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39 <when value="full"> |
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40 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" /> |
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41 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" /> |
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42 <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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43 <param name="calculate_extra_annotations" type="select" label="Calculate extra annotations, fusion splice index and interrupted index" help=""> |
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44 <option value="">Use Default</option> |
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45 <option value="no">no</option> |
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46 <option value="yes">yes</option> |
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47 </param> |
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48 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision"> |
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49 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/> |
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50 </param> |
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51 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" /> |
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52 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold"> |
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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="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" /> |
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56 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" /> |
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57 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold"> |
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58 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> |
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59 </param> |
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60 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density"> |
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61 <help>Position density when calculating covariance</help> |
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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="denovo_assembly" type="select" label="denovo_assembly" help=""> |
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65 <option value="">Use Default</option> |
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66 <option value="no">no</option> |
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67 <option value="yes">yes</option> |
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68 </param> |
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69 <!-- |
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70 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/> |
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71 --> |
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72 <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" /> |
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73 </when> <!-- full --> |
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74 </conditional> <!-- defuse_param --> |
| 5 | 75 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" |
| 76 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, | |
| 77 but they require considerable diskspace, and should be deleted and purged when no longer needed."/> | |
| 3 | 78 <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> |
| 0 | 79 </inputs> |
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80 <stdio> |
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81 <exit_code range="1:" level="fatal" description="Error Running Defuse" /> |
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82 </stdio> |
| 5 | 83 <outputs> |
| 84 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> | |
| 85 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" /> | |
| 86 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)"> | |
| 87 <filter>keep_output == True</filter> | |
| 88 </data> | |
| 89 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" /> | |
| 90 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" /> | |
| 91 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads"> | |
| 92 <filter>do_get_reads == True</filter> | |
| 93 </data> | |
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94 <!-- |
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95 expression_plot |
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96 circos plot |
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97 --> |
| 5 | 98 </outputs> |
| 0 | 99 <configfiles> |
| 100 <configfile name="defuse_config"> | |
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101 #import re |
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102 #set $ds = chr(36) |
| 0 | 103 #if $refGenomeSource.genomeSource == "history": |
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104 #set config_file = $refGenomeSource.config.__str__ |
| 0 | 105 #else |
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106 #set config_file = $refGenomeSource.index.value |
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107 #end if |
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108 #set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$' |
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109 #set fh = open($config_file) |
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110 #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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111 #set kv = [] |
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112 #for $line in $fh: |
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113 #set m = $re.match($pat,$line) |
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114 #if $m and len($m.groups()) == 2: |
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115 ## #echo $line |
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116 #if $m.groups()[0] in keys: |
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117 #set k = $m.groups()[0] |
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118 #if k == 'dataset_directory' and $refGenomeSource.genomeSource == "indexed": |
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119 ## The DataManager is conifgured to place the config file in the same directory as the defuse_data: dataset_directory |
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120 #set v = $os.path.dirname($config_file) |
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121 #else: |
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122 #set v = $m.groups()[1] |
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123 #end if |
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124 #set kv = $kv + [[$k, $v]] |
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125 #end if |
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126 #end if |
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127 #end for |
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128 ## #echo $kv |
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129 #set ref_dict = dict($kv) |
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130 ## #echo $ref_dict |
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131 ## include raw $refGenomeSource.config.__str__ |
| 0 | 132 # |
| 133 # Configuration file for defuse | |
| 134 # | |
| 135 # At a minimum, change all values enclused by [] | |
| 136 # | |
| 137 | |
| 138 # Directory where the defuse code was unpacked | |
| 139 ## Default location in the tool/defuse directory | |
| 140 # source_directory = ${__root_dir__}/tools/defuse | |
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141 source_directory = __DEFUSE_PATH__ |
| 0 | 142 |
| 143 # Directory where you want your dataset | |
| 144 dataset_directory = #slurp | |
| 145 #try | |
| 146 $ref_dict['dataset_directory'] | |
| 147 #except | |
| 148 /project/db/genomes/Hsapiens/hg19/defuse | |
| 149 #end try | |
| 150 | |
|
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151 # Organism IDs |
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152 ensembl_organism = #slurp |
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153 #try |
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154 $ref_dict['ensembl_organism'] |
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155 #except |
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156 homo_sapiens |
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157 #end try |
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158 |
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159 ensembl_prefix = #slurp |
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160 #try |
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161 $ref_dict['ensembl_prefix'] |
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162 #except |
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163 Homo_sapiens |
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164 #end try |
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165 |
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166 ensembl_version = #slurp |
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167 #try |
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168 $ref_dict['ensembl_version'] |
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169 #except |
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170 71 |
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171 #end try |
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172 |
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173 ensembl_genome_version = #slurp |
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174 #try |
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175 $ref_dict['ensembl_genome_version'] |
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176 #except |
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177 GRCh37 |
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178 #end try |
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179 |
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180 ucsc_genome_version = #slurp |
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181 #try |
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182 $ref_dict['ucsc_genome_version'] |
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183 #except |
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184 hg19 |
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185 #end try |
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186 |
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187 ncbi_organism = #slurp |
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188 #try |
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189 $ref_dict['ncbi_organism'] |
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190 #except |
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191 Homo_sapiens |
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192 #end try |
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193 |
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194 ncbi_prefix = #slurp |
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195 #try |
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196 $ref_dict['ncbi_prefix'] |
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197 #except |
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198 Hs |
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199 #end try |
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200 |
| 0 | 201 # Input genome and gene models |
| 202 gene_models = #slurp | |
| 203 #try | |
| 204 $ref_dict['gene_models'] | |
| 205 #except | |
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206 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf |
| 0 | 207 #end try |
| 208 genome_fasta = #slurp | |
| 209 #try | |
| 210 $ref_dict['genome_fasta'] | |
| 211 #except | |
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212 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa |
| 0 | 213 #end try |
| 214 | |
| 215 # Repeat table from ucsc genome browser | |
| 216 repeats_filename = #slurp | |
| 217 #try | |
| 218 $ref_dict['repeats_filename'] | |
| 219 #except | |
| 220 \$(dataset_directory)/rmsk.txt | |
| 221 #end try | |
| 222 | |
| 223 # EST info downloaded from ucsc genome browser | |
| 224 est_fasta = #slurp | |
| 225 #try | |
| 226 $ref_dict['est_fasta'] | |
| 227 #except | |
| 228 \$(dataset_directory)/est.fa | |
| 229 #end try | |
| 230 est_alignments = #slurp | |
| 231 #try | |
| 232 $ref_dict['est_alignments'] | |
| 233 #except | |
| 234 \$(dataset_directory)/intronEst.txt | |
| 235 #end try | |
| 236 | |
| 237 # Unigene clusters downloaded from ncbi | |
| 238 unigene_fasta = #slurp | |
| 239 #try | |
| 240 $ref_dict['unigene_fasta'] | |
| 241 #except | |
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242 \$(dataset_directory)/\$(ncbi_prefix).seq.uniq |
| 0 | 243 #end try |
| 244 | |
| 245 # Paths to external tools | |
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246 bowtie_bin = __BOWTIE_BIN__ |
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247 bowtie_build_bin = __BOWTIE_BUILD_BIN__ |
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248 blat_bin = __BLAT_BIN__ |
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249 fatotwobit_bin = __FATOTWOBIT_BIN__ |
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250 gmap_bin = __GMAP_BIN__ |
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251 gmap_bin = __GMAP_BIN__ |
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252 gmap_setup_bin = __GMAP_SETUP_BIN__ |
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253 r_bin = __R_BIN__ |
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254 rscript_bin = __RSCRIPT_BIN__ |
| 0 | 255 |
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256 # Directory where you want your dataset |
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257 gmap_index_directory = #slurp |
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258 #try |
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259 $ref_dict['gmap_index_directory'] |
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260 #except |
| 12 | 261 #raw |
| 262 $(dataset_directory)/gmap | |
| 263 #end raw | |
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264 #end try |
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265 |
| 0 | 266 #raw |
| 267 # Dataset files | |
| 268 dataset_prefix = $(dataset_directory)/defuse | |
| 269 chromosome_prefix = $(dataset_prefix).dna.chromosomes | |
| 270 exons_fasta = $(dataset_prefix).exons.fa | |
| 271 cds_fasta = $(dataset_prefix).cds.fa | |
| 272 cdna_regions = $(dataset_prefix).cdna.regions | |
| 273 cdna_fasta = $(dataset_prefix).cdna.fa | |
| 274 reference_fasta = $(dataset_prefix).reference.fa | |
| 275 rrna_fasta = $(dataset_prefix).rrna.fa | |
| 276 ig_gene_list = $(dataset_prefix).ig.gene.list | |
| 277 repeats_regions = $(dataset_directory)/repeats.regions | |
| 278 est_split_fasta1 = $(dataset_directory)/est.1.fa | |
| 279 est_split_fasta2 = $(dataset_directory)/est.2.fa | |
| 280 est_split_fasta3 = $(dataset_directory)/est.3.fa | |
| 281 est_split_fasta4 = $(dataset_directory)/est.4.fa | |
| 282 est_split_fasta5 = $(dataset_directory)/est.5.fa | |
| 283 est_split_fasta6 = $(dataset_directory)/est.6.fa | |
| 284 est_split_fasta7 = $(dataset_directory)/est.7.fa | |
| 285 est_split_fasta8 = $(dataset_directory)/est.8.fa | |
| 286 est_split_fasta9 = $(dataset_directory)/est.9.fa | |
| 287 | |
| 288 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs | |
| 289 prefilter1 = $(unigene_fasta) | |
| 290 | |
| 291 # deFuse scripts and tools | |
| 292 scripts_directory = $(source_directory)/scripts | |
| 293 tools_directory = $(source_directory)/tools | |
| 294 data_directory = $(source_directory)/data | |
| 295 #end raw | |
| 296 | |
| 297 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk | |
| 298 samtools_bin = #slurp | |
| 299 #try | |
| 300 $ref_dict['samtools_bin'] | |
| 301 #except | |
| 302 \$(source_directory)/external/samtools-0.1.8/samtools | |
| 303 #end try | |
| 304 | |
| 305 # Bowtie parameters | |
| 306 bowtie_threads = #slurp | |
| 307 #try | |
| 308 $ref_dict['bowtie_threads'] | |
| 309 #except | |
| 310 4 | |
| 311 #end try | |
| 312 bowtie_quals = #slurp | |
| 313 #try | |
| 314 $ref_dict['bowtie_quals'] | |
| 315 #except | |
| 316 --phred33-quals | |
| 317 #end try | |
| 318 max_insert_size = #slurp | |
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319 #if $defuse_param.settings == "full" and $defuse_param.max_insert_size.__str__ != "": |
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320 $defuse_param.max_insert_size |
| 0 | 321 #else |
| 322 #try | |
| 323 $ref_dict['max_insert_size'] | |
| 324 #except | |
| 325 500 | |
| 326 #end try | |
| 327 #end if | |
| 328 | |
| 329 # Parameters for building the dataset | |
| 330 chromosomes = #slurp | |
| 331 #try | |
| 332 $ref_dict.chromosomes | |
| 333 #except | |
| 334 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 | |
| 335 #end try | |
| 336 mt_chromosome = #slurp | |
| 337 #try | |
| 338 $ref_dict['mt_chromosome'] | |
| 339 #except | |
| 340 MT | |
| 341 #end try | |
| 342 gene_sources = #slurp | |
| 343 #try | |
| 344 $ref_dict['gene_sources'] | |
| 345 #except | |
| 346 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding | |
| 347 #end try | |
| 348 ig_gene_sources = #slurp | |
| 349 #try | |
| 350 $ref_dict['ig_gene_sources'] | |
| 351 #except | |
| 352 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene | |
| 353 #end try | |
| 354 rrna_gene_sources = #slurp | |
| 355 #try | |
| 356 $ref_dict['rrna_gene_sources'] | |
| 357 #except | |
| 358 Mt_rRNA,rRNA,rRNA_pseudogene | |
| 359 #end try | |
| 360 | |
| 361 # Blat sequences per job | |
| 362 num_blat_sequences = #slurp | |
| 363 #try | |
| 364 $ref_dict['num_blat_sequences'] | |
| 365 #except | |
| 366 10000 | |
| 367 #end try | |
| 368 | |
| 369 # Minimum gene fusion range | |
| 370 dna_concordant_length = #slurp | |
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371 #if $defuse_param.settings == "full" and $defuse_param.dna_concordant_length.__str__ != "": |
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372 $defuse_param.dna_concordant_length |
| 0 | 373 #else |
| 374 #try | |
| 375 $ref_dict['dna_concordant_length'] | |
| 376 #except | |
| 377 2000 | |
| 378 #end try | |
| 379 #end if | |
| 380 | |
| 381 # Trim length for discordant reads (split reads are not trimmed) | |
| 382 discord_read_trim = #slurp | |
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383 #if $defuse_param.settings == "full" and $defuse_param.discord_read_trim.__str__ != "": |
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384 $defuse_param.discord_read_trim |
| 0 | 385 #else |
| 386 #try | |
| 387 $ref_dict['discord_read_trim'] | |
| 388 #except | |
| 389 50 | |
| 390 #end try | |
| 391 #end if | |
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392 # Calculate extra annotations, fusion splice index and interrupted index |
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393 calculate_extra_annotations = #slurp |
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394 #if $defuse_param.settings == "full" and $defuse_param.calculate_extra_annotations.__str__ != "": |
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395 $defuse_param.calculate_extra_annotations |
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396 #else |
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397 #try |
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398 $ref_dict['calculate_extra_annotations'] |
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399 #except |
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400 no |
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401 #end try |
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402 #end if |
| 0 | 403 # Filtering parameters |
| 404 clustering_precision = #slurp | |
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405 #if $defuse_param.settings == "full" and $defuse_param.clustering_precision.__str__ != "" |
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406 $defuse_param.clustering_precision |
| 0 | 407 #else |
| 408 #try | |
| 409 $ref_dict['clustering_precision'] | |
| 410 #except | |
| 411 0.95 | |
| 412 #end try | |
| 413 #end if | |
| 414 span_count_threshold = #slurp | |
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415 #if $defuse_param.settings == "full" and $defuse_param.span_count_threshold.__str__ != "" |
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416 $defuse_param.span_count_threshold |
| 0 | 417 #else |
| 418 #try | |
| 419 $ref_dict['span_count_threshold'] | |
| 420 #except | |
| 421 5 | |
| 422 #end try | |
| 423 #end if | |
| 424 percent_identity_threshold = #slurp | |
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425 #if $defuse_param.settings == "full" and $defuse_param.percent_identity_threshold.__str__ != "" |
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426 $defuse_param.percent_identity_threshold |
| 0 | 427 #else |
| 428 #try | |
| 429 $ref_dict['percent_identity_threshold'] | |
| 430 #except | |
| 431 0.90 | |
| 432 #end try | |
| 433 #end if | |
| 434 split_min_anchor = #slurp | |
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435 #if $defuse_param.settings == "full" and $defuse_param.split_min_anchor.__str__ != "" |
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436 $defuse_param.split_min_anchor |
| 0 | 437 #else |
| 438 #try | |
| 439 $ref_dict['split_min_anchor'] | |
| 440 #except | |
| 441 4 | |
| 442 #end try | |
| 443 #end if | |
| 444 splice_bias = #slurp | |
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445 #if $defuse_param.settings == "full" and $defuse_param.splice_bias.__str__ != "" |
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446 $defuse_param.splice_bias |
| 0 | 447 #else |
| 448 #try | |
| 449 $ref_dict['splice_bias'] | |
| 450 #except | |
| 451 10 | |
| 452 #end try | |
| 453 #end if | |
| 454 denovo_assembly = #slurp | |
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455 #if $defuse_param.settings == "full" and $defuse_param.denovo_assembly.__str__ != "" |
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456 $defuse_param.denovo_assembly |
| 0 | 457 #else |
| 458 #try | |
| 459 $ref_dict['denovo_assembly'] | |
| 460 #except | |
| 461 no | |
| 462 #end try | |
| 463 #end if | |
| 464 probability_threshold = #slurp | |
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465 #if $defuse_param.settings == "full" and $defuse_param.probability_threshold.__str__ != "" |
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466 $defuse_param.probability_threshold |
| 0 | 467 #else |
| 468 #try | |
| 469 $ref_dict['probability_threshold'] | |
| 470 #except | |
| 471 0.50 | |
| 472 #end try | |
| 473 #end if | |
| 474 positive_controls = \$(data_directory)/controls.txt | |
| 475 | |
| 476 # Position density when calculating covariance | |
| 477 covariance_sampling_density = #slurp | |
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478 #if $defuse_param.settings == "full" and $defuse_param.covariance_sampling_density.__str__ != "" |
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479 $defuse_param.covariance_sampling_density |
| 0 | 480 #else |
| 481 #try | |
| 482 $ref_dict['covariance_sampling_density'] | |
| 483 #except | |
| 484 0.01 | |
| 485 #end try | |
| 486 #end if | |
| 487 # Number of reads for each job in split | |
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488 reads_per_job = #slurp |
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489 #if $defuse_param.settings == "full" and $defuse_param.reads_per_job.__str__ != "" |
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490 $defuse_param.reads_per_job |
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491 #else |
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492 #try |
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493 $ref_dict['reads_per_job'] |
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494 #except |
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495 1000000 |
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496 #end try |
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497 #end if |
| 0 | 498 |
| 499 #raw | |
| 500 # If you have command line 'mail' and wish to be notified | |
| 501 # mailto = andrew.mcpherson@gmail.com | |
| 502 | |
| 503 # Remove temp files | |
| 504 remove_job_files = yes | |
| 505 remove_job_temp_files = yes | |
| 506 | |
| 507 #end raw | |
| 508 | |
| 509 | |
| 510 </configfile> | |
| 511 <configfile name="shscript"> | |
| 512 #!/bin/bash | |
| 513 ## define some things for cheetah proccessing | |
| 514 #set $ds = chr(36) | |
| 515 #set $amp = chr(38) | |
| 516 #set $gt = chr(62) | |
| 517 #set $lt = chr(60) | |
| 518 #set $echo_cmd = 'echo' | |
| 519 ## Find the defuse.pl in the galaxy tool path | |
| 520 #import Cheetah.FileUtils | |
| 521 ## declare a bash function for converting a results tsv into html with links to the get_reads output files | |
| 522 results2html() { | |
| 523 rlts=${ds}1 | |
| 524 rslt_name=`basename ${ds}rlts` | |
| 525 html=${ds}2 | |
| 526 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse '${ds}rslt_name'${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} ${ds}html | |
| 527 echo '${lt}h2${gt}Defuse '${ds}rslt_name'${lt}/h2${gt}${lt}table${gt}' ${gt}${gt} ${ds}html | |
| 528 if [ -z "${ds}3" ] | |
| 529 then | |
| 530 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");}\ | |
| 531 ${ds}1 ~ /[1-9][0-9]*/{printf("${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} ${ds}html | |
| 532 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html | |
| 533 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html | |
| 534 else | |
| 535 export _EFP=${ds}3 | |
| 536 mkdir -p ${ds}_EFP | |
| 537 awk '${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");}\ | |
| 538 ${ds}1 ~ /[1-9][0-9]*/{fn="cluster_"${ds}1"_reads.txt"; \ | |
| 539 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} ${ds}html | |
| 540 echo '${lt}/table${gt}' ${gt}${gt} ${ds}html | |
| 541 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} ${ds}html | |
| 542 for i in `awk '${ds}1 ~ /[1-9][0-9]*/{print ${ds}1}' ${ds}rlts`; | |
| 543 do fn=cluster_${ds}{i}_reads.txt; | |
| 544 pn=${ds}_EFP/${ds}fn; | |
| 545 perl \${DEFUSE_PATH}/scripts/get_reads.pl -c $defuse_config -o output_dir -i ${ds}i ${gt} ${ds}pn; | |
| 546 done | |
| 547 fi | |
| 548 } | |
| 549 ## substitute pathnames into config file | |
| 1 | 550 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi |
| 551 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 | |
| 552 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 | |
| 553 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 | |
| 554 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 | |
| 2 | 555 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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556 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 |
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557 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 |
| 1 | 558 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 |
| 559 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 | |
| 0 | 560 |
| 561 | |
| 562 ## copy config to output | |
| 563 cp $defuse_config $config_txt | |
| 564 ## make a data_dir and ln -s the input fastq | |
| 565 mkdir -p data_dir | |
| 566 ln -s $left_pairendreads data_dir/reads_1.fastq | |
| 567 ln -s $right_pairendreads data_dir/reads_2.fastq | |
| 568 ## ln to output_dir in from_work_dir | |
| 569 #if $defuse_out.__str__ != 'None': | |
| 570 mkdir -p $defuse_out.extra_files_path | |
| 571 ln -s $defuse_out.extra_files_path output_dir | |
| 572 #else | |
| 573 mkdir -p output_dir | |
| 574 #end if | |
| 575 ## run defuse.pl | |
| 12 | 576 perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p 8 |
| 0 | 577 ## copy primary results to output datasets |
| 578 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi | |
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579 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi |
| 0 | 580 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi |
| 581 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi | |
| 582 ## create html with links for output_dir | |
| 583 #if $defuse_out.__str__ != 'None': | |
| 584 if [ -e $defuse_out ] | |
| 585 then | |
| 586 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out | |
| 587 echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out | |
| 588 pushd $defuse_out.extra_files_path | |
| 589 for f in `find -L . -maxdepth 1 -type f`; | |
| 590 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} $defuse_out; | |
| 591 done | |
| 592 popd | |
| 593 echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out | |
| 594 echo '${lt}/body${gt}${lt}/html${gt}' ${gt}${gt} $defuse_out | |
| 595 fi | |
| 596 #end if | |
| 597 ## run get_reads.pl on each cluster | |
| 598 #if $fusion_reads.__str__ != 'None': | |
| 599 if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ] | |
| 600 then | |
| 601 mkdir -p $fusion_reads.extra_files_path | |
| 602 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path | |
| 603 fi | |
| 604 #end if | |
| 605 </configfile> | |
| 606 </configfiles> | |
| 5 | 607 |
| 0 | 608 <tests> |
| 609 </tests> | |
| 610 <help> | |
| 611 **DeFuse** | |
| 612 | |
| 613 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. | |
| 614 | |
| 615 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138 | |
| 616 | |
| 617 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | |
| 618 | |
| 619 ------ | |
| 620 | |
| 621 **Inputs** | |
| 622 | |
| 623 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**). | |
| 624 | |
| 625 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. | |
| 626 | |
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627 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.4_: |
| 0 | 628 - genome_fasta from Ensembl |
| 629 - gene_models from Ensembl | |
| 630 - repeats_filename from UCSC RepeatMasker rmsk.txt | |
| 631 - est_fasta from UCSC | |
| 632 - est_alignments from UCSC intronEst.txt | |
| 633 - unigene_fasta from NCBI | |
| 634 | |
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635 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 |
| 0 | 636 |
| 637 ------ | |
| 638 | |
| 639 **Outputs** | |
| 640 | |
| 641 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. | |
| 642 | |
| 643 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. | |
| 644 | |
| 645 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order): | |
| 646 | |
| 647 - **Identification** | |
| 648 - cluster_id : random identifier assigned to each prediction | |
| 649 - library_name : library name given on the command line of defuse | |
| 650 - gene1 : ensembl id of gene 1 | |
| 651 - gene2 : ensembl id of gene 2 | |
| 652 - gene_name1 : name of gene 1 | |
| 653 - gene_name2 : name of gene 2 | |
| 654 - **Evidence** | |
| 655 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable | |
| 656 - concordant_ratio : proportion of spanning reads considered concordant by blat | |
| 657 - denovo_min_count : minimum kmer count across denovo assembled sequence | |
| 658 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly | |
| 659 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 660 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1 | |
| 661 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2 | |
| 662 - min_map_count : minimum of the number of genomic mappings for each spanning read | |
| 663 - max_map_count : maximum of the number of genomic mappings for each spanning read | |
| 664 - mean_map_count : average of the number of genomic mappings for each spanning read | |
| 665 - num_multi_map : number of spanning reads that map to more than one genomic location | |
| 666 - span_count : number of spanning reads supporting the fusion | |
| 667 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage | |
| 668 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage | |
| 669 - span_coverage_min : minimum of span_coverage1 and span_coverage2 | |
| 670 - span_coverage_max : maximum of span_coverage1 and span_coverage2 | |
| 671 - splitr_count : number of split reads supporting the prediction | |
| 672 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 673 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 674 - splitr_sequence : fusion sequence predicted by split reads | |
| 675 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 676 - **Annotation** | |
| 677 - adjacent : fusion between adjacent genes | |
| 678 - altsplice : fusion likely the product of alternative splicing between adjacent genes | |
| 679 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1 | |
| 680 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2 | |
| 681 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2 | |
| 682 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2 | |
| 683 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands | |
| 684 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna | |
| 685 - deletion : fusion produced by a genomic deletion | |
| 686 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est | |
| 687 - eversion : fusion produced by a genomic eversion | |
| 688 - exonboundaries : fusion splice at exon boundaries | |
| 689 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons | |
| 690 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons | |
| 691 - gene_chromosome1 : chromosome of gene 1 | |
| 692 - gene_chromosome2 : chromosome of gene 2 | |
| 693 - gene_end1 : end position for gene 1 | |
| 694 - gene_end2 : end position for gene 2 | |
| 695 - gene_location1 : location of breakpoint in gene 1 | |
| 696 - gene_location2 : location of breakpoint in gene 2 | |
| 697 - gene_start1 : start of gene 1 | |
| 698 - gene_start2 : start of gene 2 | |
| 699 - gene_strand1 : strand of gene 1 | |
| 700 - gene_strand2 : strand of gene 2 | |
| 701 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome | |
| 702 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint | |
| 703 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint | |
| 704 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 705 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 706 - interchromosomal : fusion produced by an interchromosomal translocation | |
| 707 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1 | |
| 708 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2 | |
| 709 - inversion : fusion produced by genomic inversion | |
| 710 - orf : fusion combines genes in a way that preserves a reading frame | |
| 711 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt) | |
| 712 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement | |
| 713 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region | |
| 714 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region | |
| 715 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2 | |
| 716 - splice_score : number of nucleotides similar to GTAG at fusion splice | |
| 717 - num_splice_variants : number of potential splice variants for this gene pair | |
| 718 - 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 | |
| 719 - 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 | |
| 720 | |
| 721 | |
| 722 **Example** | |
| 723 | |
| 724 results.tsv:: | |
| 725 | |
| 726 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 | |
| 727 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 - | |
| 728 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 - - | |
| 729 | |
| 730 </help> | |
| 731 </tool> |