Mercurial > repos > jjohnson > defuse
annotate defuse.xml @ 45:aedaa66483f1 draft
Uploaded
| author | jjohnson |
|---|---|
| date | Wed, 18 Oct 2017 16:55:57 -0400 |
| parents | 225750bf3770 |
| children | e500b50b72fd |
| rev | line source |
|---|---|
| 44 | 1 <tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.1"> |
| 2 <description>identify fusion transcripts</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <expand macro="defuse_requirement" /> | |
| 8 </requirements> | |
| 45 | 9 <command><![CDATA[ |
| 10 #if $defuse_out.__str__ != 'None': | |
| 11 ## ln to output_dir in from_work_dir | |
| 12 mkdir -p $defuse_out.dataset.extra_files_path && | |
| 13 ln -s $defuse_out.dataset.extra_files_path output_dir && | |
| 14 #else | |
| 15 mkdir -p output_dir && | |
| 16 #end if | |
| 17 ## Put executable paths in config file | |
| 18 $__tool_directory__/config_sub.sh $defuse_config output_dir/defuse.cfg && | |
| 19 ## copy config to output | |
| 20 cp defuse.cfg $config_txt && | |
| 21 ## make a data_dir and ln -s the input fastq | |
| 22 mkdir -p data_dir && | |
| 23 ln -s "$left_pairendreads" data_dir/reads_1.fastq && | |
| 24 ln -s "$right_pairendreads" data_dir/reads_2.fastq && | |
| 25 ## run | |
| 26 perl defuse_run.pl --name "$library_name" --config defuse.cfg -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS && | |
| 27 grep -v cluster_id output_dir/results.filtered.tsv | awk '{print $1}' > cluster_id_list && | |
| 28 get_fusion_fastq.pl --list cluster_id_list --output output_dir --fastq1 results.fusions_1.fq --fastq2 results.fusions_2.fq && | |
| 29 cp output_dir/results.* . && | |
| 30 cp `find output_dir -name defuse.log` $defuse_log | |
| 31 #if $defuse_out.__str__ != 'None': | |
| 32 && $__tool_directory__/make_html.sh $defuse_out $defuse_out.dataset.extra_files_path | |
| 33 #end if | |
| 34 ]]></command> | |
| 0 | 35 <inputs> |
| 36 <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.)"/> | |
| 37 <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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38 <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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39 <validator type="length" min="1"/> |
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40 </param> |
| 0 | 41 <conditional name="refGenomeSource"> |
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42 <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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43 <option value="indexed">Use a built-in DeFuse Reference Dataset</option> |
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44 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option> |
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45 </param> |
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46 <when value="indexed"> |
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47 <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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48 <options from_file="defuse_reference.loc"> |
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49 <column name="name" index="1"/> |
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50 <column name="value" index="3"/> |
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51 <filter type="sort_by" column="0" /> |
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52 <validator type="no_options" message="No indexes are available" /> |
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53 </options> |
| 0 | 54 </param> |
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55 </when> |
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56 <when value="history"> |
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57 <param name="config" type="data" format="defuse.conf" label="Defuse Config file" help=""/> |
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58 </when> <!-- history --> |
| 0 | 59 </conditional> <!-- refGenomeSource --> |
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60 <conditional name="defuse_param"> |
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61 <param name="settings" type="select" label="Defuse parameter settings" help=""> |
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62 <option value="preSet">Default settings</option> |
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63 <option value="full">Full parameter list</option> |
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64 </param> |
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65 <when value="preSet" /> |
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66 <when value="full"> |
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67 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" /> |
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68 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" /> |
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69 <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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70 <param name="calculate_extra_annotations" type="select" label="Calculate extra annotations, fusion splice index and interrupted index" help=""> |
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71 <option value="">Use Default</option> |
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72 <option value="no">no</option> |
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73 <option value="yes">yes</option> |
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74 </param> |
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75 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision"> |
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76 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/> |
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77 </param> |
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78 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" /> |
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79 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold"> |
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80 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/> |
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81 </param> |
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82 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" /> |
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83 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" /> |
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84 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold"> |
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85 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> |
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86 </param> |
| 45 | 87 <param name="multi_exon_transcripts_stats" type="select" label="Use multiple exon transcripts for stats calculations" help="should be enabled for very small libraries"> |
| 88 <option value="no" select="true">no</option> | |
| 89 <option value="yes">yes</option> | |
| 90 </param> | |
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91 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density"> |
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92 <help>Position density when calculating covariance</help> |
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93 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/> |
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94 </param> |
| 45 | 95 <param name="max_paired_alignments" type="integer" value="10" optional="true" label="max_paired_alignments"> |
| 96 <help>Maximum number of alignments for a read pair, Pairs with more alignments are filtered, default is 10</help> | |
| 97 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="1" max="100"/> | |
| 98 </param> | |
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99 <param name="denovo_assembly" type="select" label="denovo_assembly" help=""> |
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100 <option value="">Use Default</option> |
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101 <option value="no">no</option> |
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102 <option value="yes">yes</option> |
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103 </param> |
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104 <!-- |
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105 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/> |
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106 --> |
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107 <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" /> |
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108 </when> <!-- full --> |
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109 </conditional> <!-- defuse_param --> |
| 5 | 110 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" |
| 111 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, | |
| 112 but they require considerable diskspace, and should be deleted and purged when no longer needed."/> | |
| 45 | 113 <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/> |
| 44 | 114 <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> |
| 0 | 115 </inputs> |
| 5 | 116 <outputs> |
| 117 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> | |
| 118 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" /> | |
| 119 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)"> | |
| 120 <filter>keep_output == True</filter> | |
| 121 </data> | |
| 45 | 122 <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" from_work_dir="results.classify.tsv"/> |
| 123 <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" from_work_dir="results.filtered.tsv"/> | |
| 124 <data format="fastqsanger" name="results_fusions1_fq" label="${tool.name} on ${on_string}: fusions_1.fq" from_work_dir="results.fusions_1.fq" /> | |
| 125 <data format="fastqsanger" name="results_fusions2_fq" label="${tool.name} on ${on_string}: fusions_2.fq" from_work_dir="results.fusions_2.fq" /> | |
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126 <!-- |
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127 expression_plot |
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128 circos plot |
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129 --> |
| 5 | 130 </outputs> |
| 0 | 131 <configfiles> |
| 132 <configfile name="defuse_config"> | |
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133 #import re |
| 0 | 134 #if $refGenomeSource.genomeSource == "history": |
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135 #set config_file = $refGenomeSource.config.__str__ |
| 0 | 136 #else |
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137 #set config_file = $refGenomeSource.index.value |
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138 #end if |
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139 #set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$' |
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140 #set fh = open($config_file) |
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141 #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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142 #set kv = [] |
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143 #for $line in $fh: |
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144 #set m = $re.match($pat,$line) |
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145 #if $m and len($m.groups()) == 2: |
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146 ## #echo $line |
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147 #if $m.groups()[0] in keys: |
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148 #set k = $m.groups()[0] |
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149 #if k == 'dataset_directory' and $refGenomeSource.genomeSource == "indexed": |
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150 ## The DataManager is conifgured to place the config file in the same directory as the defuse_data: dataset_directory |
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151 #set v = $os.path.dirname($config_file) |
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152 #else: |
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153 #set v = $m.groups()[1] |
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154 #end if |
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155 #set kv = $kv + [[$k, $v]] |
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156 #end if |
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157 #end if |
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158 #end for |
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159 ## #echo $kv |
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160 #set ref_dict = dict($kv) |
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161 ## #echo $ref_dict |
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162 ## include raw $refGenomeSource.config.__str__ |
| 0 | 163 # |
| 164 # Configuration file for defuse | |
| 165 # | |
| 166 # At a minimum, change all values enclused by [] | |
| 167 # | |
| 168 | |
| 169 # Directory where the defuse code was unpacked | |
| 170 ## Default location in the tool/defuse directory | |
| 171 # source_directory = ${__root_dir__}/tools/defuse | |
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172 source_directory = __DEFUSE_PATH__ |
| 0 | 173 |
| 174 # Directory where you want your dataset | |
| 175 dataset_directory = #slurp | |
| 176 #try | |
| 177 $ref_dict['dataset_directory'] | |
| 178 #except | |
| 179 /project/db/genomes/Hsapiens/hg19/defuse | |
| 180 #end try | |
| 181 | |
|
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182 # Organism IDs |
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183 ensembl_organism = #slurp |
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184 #try |
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185 $ref_dict['ensembl_organism'] |
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186 #except |
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187 homo_sapiens |
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188 #end try |
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189 |
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190 ensembl_prefix = #slurp |
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191 #try |
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192 $ref_dict['ensembl_prefix'] |
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193 #except |
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194 Homo_sapiens |
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195 #end try |
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196 |
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197 ensembl_version = #slurp |
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198 #try |
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199 $ref_dict['ensembl_version'] |
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200 #except |
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201 71 |
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202 #end try |
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203 |
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204 ensembl_genome_version = #slurp |
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205 #try |
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206 $ref_dict['ensembl_genome_version'] |
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207 #except |
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208 GRCh37 |
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209 #end try |
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210 |
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211 ucsc_genome_version = #slurp |
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212 #try |
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213 $ref_dict['ucsc_genome_version'] |
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214 #except |
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215 hg19 |
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216 #end try |
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217 |
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218 ncbi_organism = #slurp |
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219 #try |
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220 $ref_dict['ncbi_organism'] |
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221 #except |
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222 Homo_sapiens |
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223 #end try |
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224 |
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225 ncbi_prefix = #slurp |
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226 #try |
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227 $ref_dict['ncbi_prefix'] |
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228 #except |
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229 Hs |
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230 #end try |
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231 |
| 0 | 232 # Input genome and gene models |
| 233 gene_models = #slurp | |
| 234 #try | |
| 235 $ref_dict['gene_models'] | |
| 236 #except | |
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237 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf |
| 0 | 238 #end try |
| 239 genome_fasta = #slurp | |
| 240 #try | |
| 241 $ref_dict['genome_fasta'] | |
| 242 #except | |
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243 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa |
| 0 | 244 #end try |
| 245 | |
| 246 # Repeat table from ucsc genome browser | |
| 247 repeats_filename = #slurp | |
| 248 #try | |
| 249 $ref_dict['repeats_filename'] | |
| 250 #except | |
| 251 \$(dataset_directory)/rmsk.txt | |
| 252 #end try | |
| 253 | |
| 254 # EST info downloaded from ucsc genome browser | |
| 255 est_fasta = #slurp | |
| 256 #try | |
| 257 $ref_dict['est_fasta'] | |
| 258 #except | |
| 259 \$(dataset_directory)/est.fa | |
| 260 #end try | |
| 261 est_alignments = #slurp | |
| 262 #try | |
| 263 $ref_dict['est_alignments'] | |
| 264 #except | |
| 265 \$(dataset_directory)/intronEst.txt | |
| 266 #end try | |
| 267 | |
| 268 # Unigene clusters downloaded from ncbi | |
| 269 unigene_fasta = #slurp | |
| 270 #try | |
| 271 $ref_dict['unigene_fasta'] | |
| 272 #except | |
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273 \$(dataset_directory)/\$(ncbi_prefix).seq.uniq |
| 0 | 274 #end try |
| 275 | |
| 276 # Paths to external tools | |
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277 bowtie_bin = __BOWTIE_BIN__ |
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278 bowtie_build_bin = __BOWTIE_BUILD_BIN__ |
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279 blat_bin = __BLAT_BIN__ |
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280 fatotwobit_bin = __FATOTWOBIT_BIN__ |
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281 gmap_bin = __GMAP_BIN__ |
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282 gmap_bin = __GMAP_BIN__ |
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283 gmap_setup_bin = __GMAP_SETUP_BIN__ |
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284 r_bin = __R_BIN__ |
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285 rscript_bin = __RSCRIPT_BIN__ |
| 0 | 286 |
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287 # Directory where you want your dataset |
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288 gmap_index_directory = #slurp |
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289 #try |
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290 $ref_dict['gmap_index_directory'] |
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291 #except |
| 12 | 292 #raw |
| 293 $(dataset_directory)/gmap | |
| 294 #end raw | |
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295 #end try |
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296 |
| 0 | 297 #raw |
| 298 # Dataset files | |
| 299 dataset_prefix = $(dataset_directory)/defuse | |
| 300 chromosome_prefix = $(dataset_prefix).dna.chromosomes | |
| 301 exons_fasta = $(dataset_prefix).exons.fa | |
| 302 cds_fasta = $(dataset_prefix).cds.fa | |
| 303 cdna_regions = $(dataset_prefix).cdna.regions | |
| 304 cdna_fasta = $(dataset_prefix).cdna.fa | |
| 305 reference_fasta = $(dataset_prefix).reference.fa | |
| 306 rrna_fasta = $(dataset_prefix).rrna.fa | |
| 307 ig_gene_list = $(dataset_prefix).ig.gene.list | |
| 308 repeats_regions = $(dataset_directory)/repeats.regions | |
| 309 est_split_fasta1 = $(dataset_directory)/est.1.fa | |
| 310 est_split_fasta2 = $(dataset_directory)/est.2.fa | |
| 311 est_split_fasta3 = $(dataset_directory)/est.3.fa | |
| 312 est_split_fasta4 = $(dataset_directory)/est.4.fa | |
| 313 est_split_fasta5 = $(dataset_directory)/est.5.fa | |
| 314 est_split_fasta6 = $(dataset_directory)/est.6.fa | |
| 315 est_split_fasta7 = $(dataset_directory)/est.7.fa | |
| 316 est_split_fasta8 = $(dataset_directory)/est.8.fa | |
| 317 est_split_fasta9 = $(dataset_directory)/est.9.fa | |
| 318 | |
| 319 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs | |
| 320 prefilter1 = $(unigene_fasta) | |
| 321 | |
| 322 # deFuse scripts and tools | |
| 323 scripts_directory = $(source_directory)/scripts | |
| 324 tools_directory = $(source_directory)/tools | |
| 325 data_directory = $(source_directory)/data | |
| 326 #end raw | |
| 327 | |
| 328 # Path to samtools, 0.1.8 is compiled for you, use other versions at your own risk | |
| 329 samtools_bin = #slurp | |
| 330 #try | |
| 331 $ref_dict['samtools_bin'] | |
| 332 #except | |
| 333 \$(source_directory)/external/samtools-0.1.8/samtools | |
| 334 #end try | |
| 335 | |
| 336 # Bowtie parameters | |
| 337 bowtie_threads = #slurp | |
| 338 #try | |
| 339 $ref_dict['bowtie_threads'] | |
| 340 #except | |
| 341 4 | |
| 342 #end try | |
| 343 bowtie_quals = #slurp | |
| 344 #try | |
| 345 $ref_dict['bowtie_quals'] | |
| 346 #except | |
| 347 --phred33-quals | |
| 348 #end try | |
| 45 | 349 bowtie_params = #slurp |
| 350 #try | |
| 351 $ref_dict['bowtie_params'] | |
| 352 #except | |
| 353 --chunkmbs 200 | |
| 354 #end try | |
| 0 | 355 max_insert_size = #slurp |
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356 #if $defuse_param.settings == "full" and $defuse_param.max_insert_size.__str__ != "": |
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357 $defuse_param.max_insert_size |
| 0 | 358 #else |
| 359 #try | |
| 360 $ref_dict['max_insert_size'] | |
| 361 #except | |
| 362 500 | |
| 363 #end try | |
| 364 #end if | |
| 365 | |
| 366 # Parameters for building the dataset | |
| 367 chromosomes = #slurp | |
| 368 #try | |
| 369 $ref_dict.chromosomes | |
| 370 #except | |
| 371 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 | |
| 372 #end try | |
| 373 mt_chromosome = #slurp | |
| 374 #try | |
| 375 $ref_dict['mt_chromosome'] | |
| 376 #except | |
| 377 MT | |
| 378 #end try | |
| 379 gene_sources = #slurp | |
| 380 #try | |
| 381 $ref_dict['gene_sources'] | |
| 382 #except | |
| 383 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding | |
| 384 #end try | |
| 385 ig_gene_sources = #slurp | |
| 386 #try | |
| 387 $ref_dict['ig_gene_sources'] | |
| 388 #except | |
| 389 IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene | |
| 390 #end try | |
| 391 rrna_gene_sources = #slurp | |
| 392 #try | |
| 393 $ref_dict['rrna_gene_sources'] | |
| 394 #except | |
| 395 Mt_rRNA,rRNA,rRNA_pseudogene | |
| 396 #end try | |
| 397 | |
| 398 # Blat sequences per job | |
| 399 num_blat_sequences = #slurp | |
| 400 #try | |
| 401 $ref_dict['num_blat_sequences'] | |
| 402 #except | |
| 403 10000 | |
| 404 #end try | |
| 405 | |
| 406 # Minimum gene fusion range | |
| 407 dna_concordant_length = #slurp | |
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408 #if $defuse_param.settings == "full" and $defuse_param.dna_concordant_length.__str__ != "": |
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409 $defuse_param.dna_concordant_length |
| 0 | 410 #else |
| 411 #try | |
| 412 $ref_dict['dna_concordant_length'] | |
| 413 #except | |
| 414 2000 | |
| 415 #end try | |
| 416 #end if | |
| 417 | |
| 418 # Trim length for discordant reads (split reads are not trimmed) | |
| 419 discord_read_trim = #slurp | |
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420 #if $defuse_param.settings == "full" and $defuse_param.discord_read_trim.__str__ != "": |
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421 $defuse_param.discord_read_trim |
| 0 | 422 #else |
| 423 #try | |
| 424 $ref_dict['discord_read_trim'] | |
| 425 #except | |
| 426 50 | |
| 427 #end try | |
| 428 #end if | |
|
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429 # Calculate extra annotations, fusion splice index and interrupted index |
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430 calculate_extra_annotations = #slurp |
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431 #if $defuse_param.settings == "full" and $defuse_param.calculate_extra_annotations.__str__ != "": |
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432 $defuse_param.calculate_extra_annotations |
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433 #else |
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434 #try |
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435 $ref_dict['calculate_extra_annotations'] |
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436 #except |
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437 no |
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438 #end try |
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439 #end if |
| 0 | 440 # Filtering parameters |
| 441 clustering_precision = #slurp | |
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442 #if $defuse_param.settings == "full" and $defuse_param.clustering_precision.__str__ != "" |
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443 $defuse_param.clustering_precision |
| 0 | 444 #else |
| 445 #try | |
| 446 $ref_dict['clustering_precision'] | |
| 447 #except | |
| 448 0.95 | |
| 449 #end try | |
| 450 #end if | |
| 451 span_count_threshold = #slurp | |
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452 #if $defuse_param.settings == "full" and $defuse_param.span_count_threshold.__str__ != "" |
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453 $defuse_param.span_count_threshold |
| 0 | 454 #else |
| 455 #try | |
| 456 $ref_dict['span_count_threshold'] | |
| 457 #except | |
| 458 5 | |
| 459 #end try | |
| 460 #end if | |
| 461 percent_identity_threshold = #slurp | |
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462 #if $defuse_param.settings == "full" and $defuse_param.percent_identity_threshold.__str__ != "" |
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463 $defuse_param.percent_identity_threshold |
| 0 | 464 #else |
| 465 #try | |
| 466 $ref_dict['percent_identity_threshold'] | |
| 467 #except | |
| 468 0.90 | |
| 469 #end try | |
| 470 #end if | |
| 471 split_min_anchor = #slurp | |
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472 #if $defuse_param.settings == "full" and $defuse_param.split_min_anchor.__str__ != "" |
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473 $defuse_param.split_min_anchor |
| 0 | 474 #else |
| 475 #try | |
| 476 $ref_dict['split_min_anchor'] | |
| 477 #except | |
| 478 4 | |
| 479 #end try | |
| 480 #end if | |
| 481 splice_bias = #slurp | |
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482 #if $defuse_param.settings == "full" and $defuse_param.splice_bias.__str__ != "" |
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483 $defuse_param.splice_bias |
| 0 | 484 #else |
| 485 #try | |
| 486 $ref_dict['splice_bias'] | |
| 487 #except | |
| 488 10 | |
| 489 #end try | |
| 490 #end if | |
| 491 denovo_assembly = #slurp | |
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492 #if $defuse_param.settings == "full" and $defuse_param.denovo_assembly.__str__ != "" |
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493 $defuse_param.denovo_assembly |
| 0 | 494 #else |
| 495 #try | |
| 496 $ref_dict['denovo_assembly'] | |
| 497 #except | |
| 498 no | |
| 499 #end try | |
| 500 #end if | |
| 501 probability_threshold = #slurp | |
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502 #if $defuse_param.settings == "full" and $defuse_param.probability_threshold.__str__ != "" |
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503 $defuse_param.probability_threshold |
| 0 | 504 #else |
| 505 #try | |
| 506 $ref_dict['probability_threshold'] | |
| 507 #except | |
| 508 0.50 | |
| 509 #end try | |
| 510 #end if | |
| 511 positive_controls = \$(data_directory)/controls.txt | |
| 512 | |
| 45 | 513 # Use multiple exon transcripts for stats calculations (yes/no) |
| 514 # should be enabled for very small libraries | |
| 515 multi_exon_transcripts_stats = #slurp | |
| 516 #if $defuse_param.settings == "full" and $defuse_param.multi_exon_transcripts_stats.__str__ != "" | |
| 517 $defuse_param.multi_exon_transcripts_stats | |
| 518 #else | |
| 519 #try | |
| 520 $ref_dict['multi_exon_transcripts_stats'] | |
| 521 #except | |
| 522 no | |
| 523 #end try | |
| 524 #end if | |
| 525 | |
| 0 | 526 # Position density when calculating covariance |
| 527 covariance_sampling_density = #slurp | |
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528 #if $defuse_param.settings == "full" and $defuse_param.covariance_sampling_density.__str__ != "" |
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529 $defuse_param.covariance_sampling_density |
| 0 | 530 #else |
| 531 #try | |
| 532 $ref_dict['covariance_sampling_density'] | |
| 533 #except | |
| 534 0.01 | |
| 535 #end try | |
| 536 #end if | |
| 45 | 537 |
| 538 # Maximum number of alignments for a read pair | |
| 539 # Pairs with more alignments are filtered | |
| 540 max_paired_alignments = #slurp | |
| 541 #if $defuse_param.settings == "full" and $defuse_param.max_paired_alignments.__str__ != "" | |
| 542 $defuse_param.max_paired_alignments | |
| 543 #else | |
| 544 #try | |
| 545 $ref_dict['max_paired_alignments'] | |
| 546 #except | |
| 547 10 | |
| 548 #end try | |
| 549 #end if | |
| 550 | |
| 0 | 551 # Number of reads for each job in split |
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552 reads_per_job = #slurp |
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553 #if $defuse_param.settings == "full" and $defuse_param.reads_per_job.__str__ != "" |
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554 $defuse_param.reads_per_job |
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555 #else |
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556 #try |
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557 $ref_dict['reads_per_job'] |
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558 #except |
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559 1000000 |
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560 #end try |
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561 #end if |
| 0 | 562 |
| 563 #raw | |
| 564 # If you have command line 'mail' and wish to be notified | |
| 565 # mailto = andrew.mcpherson@gmail.com | |
| 566 | |
| 567 # Remove temp files | |
| 568 remove_job_files = yes | |
| 569 remove_job_temp_files = yes | |
| 570 | |
| 45 | 571 qsub_params = "" |
| 572 | |
| 0 | 573 #end raw |
| 574 | |
| 575 </configfile> | |
| 576 </configfiles> | |
| 5 | 577 |
| 0 | 578 <tests> |
| 579 </tests> | |
| 580 <help> | |
| 581 **DeFuse** | |
| 582 | |
| 583 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. | |
| 584 | |
| 585 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138 | |
| 586 | |
| 587 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | |
| 588 | |
| 589 ------ | |
| 590 | |
| 591 **Inputs** | |
| 592 | |
| 593 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**). | |
| 594 | |
| 595 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. | |
| 596 | |
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597 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 | 598 - genome_fasta from Ensembl |
| 599 - gene_models from Ensembl | |
| 600 - repeats_filename from UCSC RepeatMasker rmsk.txt | |
| 601 - est_fasta from UCSC | |
| 602 - est_alignments from UCSC intronEst.txt | |
| 603 - unigene_fasta from NCBI | |
| 604 | |
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605 .. _DeFuse_Version_0.4: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 |
| 0 | 606 |
| 607 ------ | |
| 608 | |
| 609 **Outputs** | |
| 610 | |
| 611 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. | |
| 612 | |
| 613 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. | |
| 614 | |
| 615 The file format is tab delimited with one prediction per line, and the following fields per prediction (not necessarily in this order): | |
| 616 | |
| 617 - **Identification** | |
| 618 - cluster_id : random identifier assigned to each prediction | |
| 619 - library_name : library name given on the command line of defuse | |
| 620 - gene1 : ensembl id of gene 1 | |
| 621 - gene2 : ensembl id of gene 2 | |
| 622 - gene_name1 : name of gene 1 | |
| 623 - gene_name2 : name of gene 2 | |
| 624 - **Evidence** | |
| 625 - break_predict : breakpoint prediction method, denovo or splitr, that is considered most reliable | |
| 626 - concordant_ratio : proportion of spanning reads considered concordant by blat | |
| 627 - denovo_min_count : minimum kmer count across denovo assembled sequence | |
| 628 - denovo_sequence : fusion sequence predicted by debruijn based denovo sequence assembly | |
| 629 - denovo_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 630 - gene_align_strand1 : alignment strand for spanning read alignments to gene 1 | |
| 631 - gene_align_strand2 : alignment strand for spanning read alignments to gene 2 | |
| 632 - min_map_count : minimum of the number of genomic mappings for each spanning read | |
| 633 - max_map_count : maximum of the number of genomic mappings for each spanning read | |
| 634 - mean_map_count : average of the number of genomic mappings for each spanning read | |
| 635 - num_multi_map : number of spanning reads that map to more than one genomic location | |
| 636 - span_count : number of spanning reads supporting the fusion | |
| 637 - span_coverage1 : coverage of spanning reads aligned to gene 1 as a proportion of expected coverage | |
| 638 - span_coverage2 : coverage of spanning reads aligned to gene 2 as a proportion of expected coverage | |
| 639 - span_coverage_min : minimum of span_coverage1 and span_coverage2 | |
| 640 - span_coverage_max : maximum of span_coverage1 and span_coverage2 | |
| 641 - splitr_count : number of split reads supporting the prediction | |
| 642 - splitr_min_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 643 - splitr_pos_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 644 - splitr_sequence : fusion sequence predicted by split reads | |
| 645 - splitr_span_pvalue : p-value, lower values are evidence the prediction is a false positive | |
| 646 - **Annotation** | |
| 647 - adjacent : fusion between adjacent genes | |
| 648 - altsplice : fusion likely the product of alternative splicing between adjacent genes | |
| 649 - break_adj_entropy1 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 1 | |
| 650 - break_adj_entropy2 : di-nucleotide entropy of the 40 nucleotides adjacent to the fusion splice in gene 2 | |
| 651 - break_adj_entropy_min : minimum of break_adj_entropy1 and break_adj_entropy2 | |
| 652 - breakpoint_homology : number of nucleotides at the fusion splice that align equally well to gene 1 or gene 2 | |
| 653 - breakseqs_estislands_percident : maximum percent identity of fusion sequence alignments to est islands | |
| 654 - cdna_breakseqs_percident : maximum percent identity of fusion sequence alignments to cdna | |
| 655 - deletion : fusion produced by a genomic deletion | |
| 656 - est_breakseqs_percident : maximum percent identity of fusion sequence alignments to est | |
| 657 - eversion : fusion produced by a genomic eversion | |
| 658 - exonboundaries : fusion splice at exon boundaries | |
| 659 - expression1 : expression of gene 1 as number of concordant pairs aligned to exons | |
| 660 - expression2 : expression of gene 2 as number of concordant pairs aligned to exons | |
| 661 - gene_chromosome1 : chromosome of gene 1 | |
| 662 - gene_chromosome2 : chromosome of gene 2 | |
| 663 - gene_end1 : end position for gene 1 | |
| 664 - gene_end2 : end position for gene 2 | |
| 665 - gene_location1 : location of breakpoint in gene 1 | |
| 666 - gene_location2 : location of breakpoint in gene 2 | |
| 667 - gene_start1 : start of gene 1 | |
| 668 - gene_start2 : start of gene 2 | |
| 669 - gene_strand1 : strand of gene 1 | |
| 670 - gene_strand2 : strand of gene 2 | |
| 671 - genome_breakseqs_percident : maximum percent identity of fusion sequence alignments to genome | |
| 672 - genomic_break_pos1 : genomic position in gene 1 of fusion splice / breakpoint | |
| 673 - genomic_break_pos2 : genomic position in gene 2 of fusion splice / breakpoint | |
| 674 - genomic_strand1 : genomic strand in gene 1 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 675 - genomic_strand2 : genomic strand in gene 2 of fusion splice / breakpoint, retained sequence upstream on this strand, breakpoint is downstream | |
| 676 - interchromosomal : fusion produced by an interchromosomal translocation | |
| 677 - interrupted_index1 : ratio of coverage before and after the fusion splice / breakpoint in gene 1 | |
| 678 - interrupted_index2 : ratio of coverage before and after the fusion splice / breakpoint in gene 2 | |
| 679 - inversion : fusion produced by genomic inversion | |
| 680 - orf : fusion combines genes in a way that preserves a reading frame | |
| 681 - probability : probability produced by classification using adaboost and example positives/negatives (only given in results.classified.txt) | |
| 682 - read_through : fusion involving adjacent potentially resulting from co-transcription rather than genome rearrangement | |
| 683 - repeat_proportion1 : proportion of the spanning reads in gene 1 that span a repeat region | |
| 684 - repeat_proportion2 : proportion of the spanning reads in gene 2 that span a repeat region | |
| 685 - max_repeat_proportion : max of repeat_proportion1 and repeat_proportion2 | |
| 686 - splice_score : number of nucleotides similar to GTAG at fusion splice | |
| 687 - num_splice_variants : number of potential splice variants for this gene pair | |
| 688 - 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 | |
| 689 - 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 | |
| 690 | |
| 691 | |
| 692 **Example** | |
| 693 | |
| 694 results.tsv:: | |
| 695 | |
| 696 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 | |
| 697 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 - | |
| 698 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 - - | |
| 699 | |
| 700 </help> | |
| 44 | 701 <expand macro="citations"/> |
| 0 | 702 </tool> |