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comparison defuse.xml @ 11:b22f8634ff84 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
parents f65857c1b92e
children 4fe2e80d4ae1
comparison
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10:f65857c1b92e 11:b22f8634ff84
1 <tool id="defuse" name="DeFuse" version="1.6"> 1 <tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.1">
2 <description>identify fusion transcripts</description> 2 <description>identify fusion transcripts</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.6.0">defuse</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="0.1.18">samtools</requirement> 5 </macros>
6 <requirement type="package" version="0.12.7">bowtie</requirement> 6 <requirements>
7 <requirement type="package" version="2012-07-20">gmap</requirement> 7 <expand macro="defuse_requirement" />
8 <requirement type="package" version="34x10">blat</requirement> 8 <expand macro="mapping_requirements" />
9 <requirement type="package" version="34x10">fatotwobit</requirement> 9 <expand macro="r_requirements" />
10 </requirements> 10 </requirements>
11 <command interpreter="command"> /bin/bash $shscript </command> 11 <command interpreter="command"> /bin/bash $shscript </command>
12 <inputs> 12 <inputs>
13 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/> 13 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/>
14 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/> 14 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
15 <param name="library_name" type="text" value="unknown" label="library name" help="Value to put in the results library_name column">
16 <validator type="length" min="1"/>
17 </param>
15 <conditional name="refGenomeSource"> 18 <conditional name="refGenomeSource">
16 <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help=""> 19 <param name="genomeSource" type="select" label="Will you select a built-in DeFuse Reference Dataset, or supply a configuration from your history" help="">
17 <option value="indexed">Use a built-in DeFuse Reference Dataset</option> 20 <option value="indexed">Use a built-in DeFuse Reference Dataset</option>
18 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option> 21 <option value="history">Use a configuration from your history that specifies the DeFuse Reference Dataset</option>
19 </param> 22 </param>
20 <when value="indexed"> 23 <when value="indexed">
21 <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team"> 24 <param name="index" type="select" label="Select a Reference Dataset" help="if your genome of interest is not listed - contact Galaxy team">
22 <options from_file="defuse.loc"> 25 <options from_file="defuse_reference.loc">
23 <column name="name" index="1"/> 26 <column name="name" index="1"/>
24 <column name="value" index="2"/> 27 <column name="value" index="3"/>
25 <filter type="sort_by" column="0" /> 28 <filter type="sort_by" column="0" />
26 <validator type="no_options" message="No indexes are available" /> 29 <validator type="no_options" message="No indexes are available" />
27 </options> 30 </options>
28 </param> 31 </param>
29 <conditional name="defuse_param"> 32 </when>
30 <param name="settings" type="select" label="Defuse parameter settings" help=""> 33 <when value="history">
31 <option value="preSet">Default settings</option> 34 <param name="config" type="data" format="defuse.conf" label="Defuse Config file" help=""/>
32 <option value="full">Full parameter list</option> 35 </when> <!-- history -->
33 </param>
34 <when value="preSet" />
35 <when value="full">
36 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
37 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
38 <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)" />
39 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
40 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
41 </param>
42 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
43 <param name="split_count_threshold" type="integer" value="3" optional="true" label="Filter split_count_threshold" />
44 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
45 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
46 </param>
47 <param name="max_dist_pos" type="integer" value="600" optional="true" label="Filter max_dist_pos" />
48 <param name="num_dist_genes" type="integer" value="500" optional="true" label="Filter num_dist_genes" />
49 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
50 <param name="max_concordant_ratio" type="float" value="0.1" optional="true" label="Filter max_concordant_ratio">
51 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
52 </param>
53 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
54 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
55 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
56 </param>
57 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
58 <help>Position density when calculating covariance</help>
59 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
60 </param>
61 <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
62 <option value="">Use Default</option>
63 <option value="no">no</option>
64 <option value="yes">yes</option>
65 </param>
66 <!--
67 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
68 -->
69 </when> <!-- full -->
70 </conditional> <!-- defuse_param -->
71 </when>
72 <when value="history">
73 <param name="config" type="data" format="txt" label="Defuse Config file" help=""/>
74 </when> <!-- history -->
75 </conditional> <!-- refGenomeSource --> 36 </conditional> <!-- refGenomeSource -->
37 <conditional name="defuse_param">
38 <param name="settings" type="select" label="Defuse parameter settings" help="">
39 <option value="preSet">Default settings</option>
40 <option value="full">Full parameter list</option>
41 </param>
42 <when value="preSet" />
43 <when value="full">
44 <param name="max_insert_size" type="integer" value="500" optional="true" label="Bowtie max_insert_size" />
45 <param name="dna_concordant_length" type="integer" value="2000" optional="true" label="Minimum gene fusion range dna_concordant_length" />
46 <param name="discord_read_trim" type="integer" value="50" optional="true" label="Trim length for discordant reads discord_read_trim" help="(split reads are not trimmed)" />
47 <param name="calculate_extra_annotations" type="select" label="Calculate extra annotations, fusion splice index and interrupted index" help="">
48 <option value="">Use Default</option>
49 <option value="no">no</option>
50 <option value="yes">yes</option>
51 </param>
52 <param name="clustering_precision" type="float" value=".95" optional="true" label="Filter clustering_precision">
53 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
54 </param>
55 <param name="span_count_threshold" type="integer" value="5" optional="true" label="Filter span_count_threshold" />
56 <param name="percent_identity_threshold" type="float" value=".90" optional="true" label="Filter percent_identity_threshold">
57 <validator type="in_range" message="Choose a value between .1 and 1.0" min=".1" max="1"/>
58 </param>
59 <param name="split_min_anchor" type="integer" value="4" optional="true" label="Filter split_min_anchor" />
60 <param name="splice_bias" type="integer" value="10" optional="true" label="Filter splice_bias" />
61 <param name="probability_threshold" type="float" value="0.50" optional="true" label="Filter probability_threshold">
62 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
63 </param>
64 <param name="multi_exon_transcripts_stats" type="select" label="Use multiple exon transcripts for stats calculations" help="should be enabled for very small libraries">
65 <option value="no" select="true">no</option>
66 <option value="yes">yes</option>
67 </param>
68 <param name="covariance_sampling_density" type="float" value="0.01" optional="true" label="covariance_sampling_density">
69 <help>Position density when calculating covariance</help>
70 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="0" max="1"/>
71 </param>
72 <param name="max_paired_alignments" type="integer" value="10" optional="true" label="max_paired_alignments">
73 <help>Maximum number of alignments for a read pair, Pairs with more alignments are filtered, default is 10</help>
74 <validator type="in_range" message="Choose a value between 0.0 and 1.0" min="1" max="100"/>
75 </param>
76 <param name="denovo_assembly" type="select" label="denovo_assembly" help="">
77 <option value="">Use Default</option>
78 <option value="no">no</option>
79 <option value="yes">yes</option>
80 </param>
81 <!--
82 <param name="positive_controls" type="data" format="txt" optional=true label="Defuse positive_controls" help=""/>
83 -->
84 <param name="reads_per_job" type="integer" value="1000000" optional="true" label="Number of reads for each job in split" />
85 </when> <!-- full -->
86 </conditional> <!-- defuse_param -->
87 <param name="breakpoints_bam" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
76 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 88 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"
77 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 89 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run,
78 but they require considerable diskspace, and should be deleted and purged when no longer needed."/> 90 but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
79 <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/> 91 <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
80 </inputs> 92 </inputs>
93 <stdio>
94 <exit_code range="1:" level="fatal" description="Error Running Defuse" />
95 </stdio>
81 <outputs> 96 <outputs>
82 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> 97 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
83 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" /> 98 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
84 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)"> 99 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">
85 <filter>keep_output == True</filter> 100 <filter>keep_output == True</filter>
86 </data> 101 </data>
87 <data format="tabular" name="results_tsv" label="${tool.name} on ${on_string}: results.tsv" /> 102 <data format="defuse.results.tsv" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" />
88 <data format="tabular" name="results_classify_tsv" label="${tool.name} on ${on_string}: results.classify.tsv" /> 103 <data format="defuse.results.tsv" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
89 <data format="tabular" name="results_filtered_tsv" label="${tool.name} on ${on_string}: results.filtered.tsv" />
90 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads"> 104 <data format="html" name="fusion_reads" label="${tool.name} on ${on_string}: fusion_reads">
91 <filter>do_get_reads == True</filter> 105 <filter>do_get_reads == True</filter>
92 </data> 106 </data>
107 <data format="bam" name="fusions_bam" label="${tool.name} on ${on_string}: fusions.bam">
108 <filter>breakpoints_bam == True</filter>
109 </data>
110 <!--
111 expression_plot
112 circos plot
113 -->
93 </outputs> 114 </outputs>
94 <configfiles> 115 <configfiles>
95 <configfile name="defuse_config"> 116 <configfile name="defuse_config">
96 #import ast 117 #import re
118 #set $ds = chr(36)
97 #if $refGenomeSource.genomeSource == "history": 119 #if $refGenomeSource.genomeSource == "history":
98 #include raw $refGenomeSource.config.__str__ 120 #set config_file = $refGenomeSource.config.__str__
99 #else 121 #else
100 #set $ref_dict = dict($ast.literal_eval($refGenomeSource.index.value)) 122 #set config_file = $refGenomeSource.index.value
123 #end if
124 #set pat = '^\s*([^#=][^=]*?)\s*=\s*(.*?)\s*$'
125 #set fh = open($config_file)
126 #set keys = ['dataset_directory','ensembl_organism','ensembl_prefix','ensembl_version','ensembl_genome_version','ucsc_genome_version','ncbi_organism','ncbi_prefix','chromosomes','mt_chromosome','gene_sources','ig_gene_sources','rrna_gene_sources']
127 #set kv = []
128 #for $line in $fh:
129 #set m = $re.match($pat,$line)
130 #if $m and len($m.groups()) == 2:
131 ## #echo $line
132 #if $m.groups()[0] in keys:
133 #set k = $m.groups()[0]
134 #if k == 'dataset_directory' and $refGenomeSource.genomeSource == "indexed":
135 ## The DataManager is conifgured to place the config file in the same directory as the defuse_data: dataset_directory
136 #set v = $os.path.dirname($config_file)
137 #else:
138 #set v = $m.groups()[1]
139 #end if
140 #set kv = $kv + [[$k, $v]]
141 #end if
142 #end if
143 #end for
144 ## #echo $kv
145 #set ref_dict = dict($kv)
146 ## #echo $ref_dict
147 ## include raw $refGenomeSource.config.__str__
101 # 148 #
102 # Configuration file for defuse 149 # Configuration file for defuse
103 # 150 #
104 # At a minimum, change all values enclused by [] 151 # At a minimum, change all values enclused by []
105 # 152 #
106 153
107 # Directory where the defuse code was unpacked 154 # Directory where the defuse code was unpacked
108 ## Default location in the tool/defuse directory 155 ## Default location in the tool/defuse directory
109 # source_directory = ${__root_dir__}/tools/defuse 156 # source_directory = ${__root_dir__}/tools/defuse
110 source_directory = #slurp 157 source_directory = __DEFUSE_PATH__
111 #try
112 $ref_dict['source_directory']
113 #except
114 __DEFUSE_PATH__
115 #end try
116 158
117 # Directory where you want your dataset 159 # Directory where you want your dataset
118 dataset_directory = #slurp 160 dataset_directory = #slurp
119 #try 161 #try
120 $ref_dict['dataset_directory'] 162 $ref_dict['dataset_directory']
121 #except 163 #except
122 /project/db/genomes/Hsapiens/hg19/defuse 164 /project/db/genomes/Hsapiens/hg19/defuse
123 #end try 165 #end try
124 166
167 # Organism IDs
168 ensembl_organism = #slurp
169 #try
170 $ref_dict['ensembl_organism']
171 #except
172 homo_sapiens
173 #end try
174
175 ensembl_prefix = #slurp
176 #try
177 $ref_dict['ensembl_prefix']
178 #except
179 Homo_sapiens
180 #end try
181
182 ensembl_version = #slurp
183 #try
184 $ref_dict['ensembl_version']
185 #except
186 71
187 #end try
188
189 ensembl_genome_version = #slurp
190 #try
191 $ref_dict['ensembl_genome_version']
192 #except
193 GRCh37
194 #end try
195
196 ucsc_genome_version = #slurp
197 #try
198 $ref_dict['ucsc_genome_version']
199 #except
200 hg19
201 #end try
202
203 ncbi_organism = #slurp
204 #try
205 $ref_dict['ncbi_organism']
206 #except
207 Homo_sapiens
208 #end try
209
210 ncbi_prefix = #slurp
211 #try
212 $ref_dict['ncbi_prefix']
213 #except
214 Hs
215 #end try
216
125 # Input genome and gene models 217 # Input genome and gene models
126 gene_models = #slurp 218 gene_models = #slurp
127 #try 219 #try
128 $ref_dict['gene_models'] 220 $ref_dict['gene_models']
129 #except 221 #except
130 \$(dataset_directory)/Homo_sapiens.GRCh37.62.gtf 222 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).gtf
131 #end try 223 #end try
132 genome_fasta = #slurp 224 genome_fasta = #slurp
133 #try 225 #try
134 $ref_dict['genome_fasta'] 226 $ref_dict['genome_fasta']
135 #except 227 #except
136 \$(dataset_directory)/Homo_sapiens.GRCh37.62.dna.chromosome.fa 228 \$(dataset_directory)/\$(ensembl_prefix).\$(ensembl_genome_version).\$(ensembl_version).dna.chromosomes.fa
137 #end try 229 #end try
138 230
139 # Repeat table from ucsc genome browser 231 # Repeat table from ucsc genome browser
140 repeats_filename = #slurp 232 repeats_filename = #slurp
141 #try 233 #try
161 # Unigene clusters downloaded from ncbi 253 # Unigene clusters downloaded from ncbi
162 unigene_fasta = #slurp 254 unigene_fasta = #slurp
163 #try 255 #try
164 $ref_dict['unigene_fasta'] 256 $ref_dict['unigene_fasta']
165 #except 257 #except
166 \$(dataset_directory)/Hs.seq.uniq 258 \$(dataset_directory)/\$(ncbi_prefix).seq.uniq
167 #end try 259 #end try
168 260
169 # Paths to external tools 261 # Paths to external tools
170 bowtie_bin = #slurp 262 bowtie_bin = __BOWTIE_BIN__
171 #try 263 bowtie_build_bin = __BOWTIE_BUILD_BIN__
172 $ref_dict['bowtie_bin'] 264 blat_bin = __BLAT_BIN__
173 #except 265 fatotwobit_bin = __FATOTWOBIT_BIN__
174 __BOWTIE_BIN__ 266 gmap_bin = __GMAP_BIN__
175 #end try 267 gmap_bin = __GMAP_BIN__
176 bowtie_build_bin = #slurp 268 gmap_setup_bin = __GMAP_SETUP_BIN__
177 #try 269 r_bin = __R_BIN__
178 $ref_dict['bowtie_build_bin'] 270 rscript_bin = __RSCRIPT_BIN__
179 #except
180 __BOWTIE_BUILD_BIN__
181 #end try
182 blat_bin = #slurp
183 #try
184 $ref_dict['blat_bin']
185 #except
186 __BLAT_BIN__
187 #end try
188 fatotwobit_bin = #slurp
189 #try
190 $ref_dict['fatotwobit_bin']
191 #except
192 __FATOTWOBIT_BIN__
193 #end try
194 gmap_bin = #slurp
195 #try
196 $ref_dict['gmap_bin']
197 #except
198 __GMAP_BIN__
199 #end try
200 gmap_bin = #slurp
201 #try
202 $ref_dict['gmap_bin']
203 #except
204 __GMAP_BIN__
205 #end try
206 gmap_setup_bin = #slurp
207 #try
208 $ref_dict['gmap_setup_bin']
209 #except
210 __GMAP_SETUP_BIN__
211 #end try
212 r_bin = #slurp
213 #try
214 $ref_dict['r_bin']
215 #except
216 __R_BIN__
217 #end try
218 rscript_bin = #slurp
219 #try
220 $ref_dict['rscript_bin']
221 #except
222 __RSCRIPT_BIN__
223 #end try
224 271
225 # Directory where you want your dataset 272 # Directory where you want your dataset
226 gmap_index_directory = #slurp 273 gmap_index_directory = #slurp
227 #try 274 #try
228 $ref_dict['gmap_index_directory'] 275 $ref_dict['gmap_index_directory']
229 #except 276 #except
230 \$(dataset_directory)/gmap 277 #raw
278 $(dataset_directory)/gmap
279 #end raw
231 #end try 280 #end try
232 281
233 #raw 282 #raw
234 # Dataset files 283 # Dataset files
235 dataset_prefix = $(dataset_directory)/defuse 284 dataset_prefix = $(dataset_directory)/defuse
280 #try 329 #try
281 $ref_dict['bowtie_quals'] 330 $ref_dict['bowtie_quals']
282 #except 331 #except
283 --phred33-quals 332 --phred33-quals
284 #end try 333 #end try
334 bowtie_params = #slurp
335 #try
336 $ref_dict['bowtie_params']
337 #except
338 --chunkmbs 200
339 #end try
285 max_insert_size = #slurp 340 max_insert_size = #slurp
286 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_insert_size.__str__ != "": 341 #if $defuse_param.settings == "full" and $defuse_param.max_insert_size.__str__ != "":
287 $refGenomeSource.defuse_param.max_insert_size 342 $defuse_param.max_insert_size
288 #else 343 #else
289 #try 344 #try
290 $ref_dict['max_insert_size'] 345 $ref_dict['max_insert_size']
291 #except 346 #except
292 500 347 500
333 10000 388 10000
334 #end try 389 #end try
335 390
336 # Minimum gene fusion range 391 # Minimum gene fusion range
337 dna_concordant_length = #slurp 392 dna_concordant_length = #slurp
338 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.dna_concordant_length.__str__ != "": 393 #if $defuse_param.settings == "full" and $defuse_param.dna_concordant_length.__str__ != "":
339 $refGenomeSource.defuse_param.dna_concordant_length 394 $defuse_param.dna_concordant_length
340 #else 395 #else
341 #try 396 #try
342 $ref_dict['dna_concordant_length'] 397 $ref_dict['dna_concordant_length']
343 #except 398 #except
344 2000 399 2000
345 #end try 400 #end try
346 #end if 401 #end if
347 402
348 # Trim length for discordant reads (split reads are not trimmed) 403 # Trim length for discordant reads (split reads are not trimmed)
349 discord_read_trim = #slurp 404 discord_read_trim = #slurp
350 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.discord_read_trim.__str__ != "": 405 #if $defuse_param.settings == "full" and $defuse_param.discord_read_trim.__str__ != "":
351 $refGenomeSource.defuse_param.discord_read_trim 406 $defuse_param.discord_read_trim
352 #else 407 #else
353 #try 408 #try
354 $ref_dict['discord_read_trim'] 409 $ref_dict['discord_read_trim']
355 #except 410 #except
356 50 411 50
357 #end try 412 #end try
358 #end if 413 #end if
359 414 # Calculate extra annotations, fusion splice index and interrupted index
415 calculate_extra_annotations = #slurp
416 #if $defuse_param.settings == "full" and $defuse_param.calculate_extra_annotations.__str__ != "":
417 $defuse_param.calculate_extra_annotations
418 #else
419 #try
420 $ref_dict['calculate_extra_annotations']
421 #except
422 no
423 #end try
424 #end if
360 # Filtering parameters 425 # Filtering parameters
361 clustering_precision = #slurp 426 clustering_precision = #slurp
362 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.clustering_precision.__str__ != "" 427 #if $defuse_param.settings == "full" and $defuse_param.clustering_precision.__str__ != ""
363 $refGenomeSource.defuse_param.clustering_precision 428 $defuse_param.clustering_precision
364 #else 429 #else
365 #try 430 #try
366 $ref_dict['clustering_precision'] 431 $ref_dict['clustering_precision']
367 #except 432 #except
368 0.95 433 0.95
369 #end try 434 #end try
370 #end if 435 #end if
371 span_count_threshold = #slurp 436 span_count_threshold = #slurp
372 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.span_count_threshold.__str__ != "" 437 #if $defuse_param.settings == "full" and $defuse_param.span_count_threshold.__str__ != ""
373 $refGenomeSource.defuse_param.span_count_threshold 438 $defuse_param.span_count_threshold
374 #else 439 #else
375 #try 440 #try
376 $ref_dict['span_count_threshold'] 441 $ref_dict['span_count_threshold']
377 #except 442 #except
378 5 443 5
379 #end try 444 #end try
380 #end if 445 #end if
381 split_count_threshold = #slurp
382 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_count_threshold.__str__ != ""
383 $refGenomeSource.defuse_param.split_count_threshold
384 #else
385 #try
386 $ref_dict['split_count_threshold']
387 #except
388 3
389 #end try
390 #end if
391 percent_identity_threshold = #slurp 446 percent_identity_threshold = #slurp
392 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.percent_identity_threshold.__str__ != "" 447 #if $defuse_param.settings == "full" and $defuse_param.percent_identity_threshold.__str__ != ""
393 $refGenomeSource.defuse_param.percent_identity_threshold 448 $defuse_param.percent_identity_threshold
394 #else 449 #else
395 #try 450 #try
396 $ref_dict['percent_identity_threshold'] 451 $ref_dict['percent_identity_threshold']
397 #except 452 #except
398 0.90 453 0.90
399 #end try 454 #end try
400 #end if 455 #end if
401 max_dist_pos = #slurp
402 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_dist_pos.__str__ != ""
403 $refGenomeSource.defuse_param.max_dist_pos
404 #else
405 #try
406 $ref_dict['max_dist_pos']
407 #except
408 600
409 #end try
410 #end if
411 num_dist_genes = #slurp
412 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.num_dist_genes.__str__ != ""
413 $refGenomeSource.defuse_param.num_dist_genes
414 #else
415 #try
416 $ref_dict['num_dist_genes']
417 #except
418 500
419 #end try
420 #end if
421 split_min_anchor = #slurp 456 split_min_anchor = #slurp
422 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.split_min_anchor.__str__ != "" 457 #if $defuse_param.settings == "full" and $defuse_param.split_min_anchor.__str__ != ""
423 $refGenomeSource.defuse_param.split_min_anchor 458 $defuse_param.split_min_anchor
424 #else 459 #else
425 #try 460 #try
426 $ref_dict['split_min_anchor'] 461 $ref_dict['split_min_anchor']
427 #except 462 #except
428 4 463 4
429 #end try 464 #end try
430 #end if 465 #end if
431 max_concordant_ratio = #slurp
432 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.max_concordant_ratio.__str__ != ""
433 $refGenomeSource.defuse_param.max_concordant_ratio
434 #else
435 #try
436 $ref_dict['max_concordant_ratio']
437 #except
438 0.1
439 #end try
440 #end if
441 splice_bias = #slurp 466 splice_bias = #slurp
442 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.splice_bias.__str__ != "" 467 #if $defuse_param.settings == "full" and $defuse_param.splice_bias.__str__ != ""
443 $refGenomeSource.defuse_param.splice_bias 468 $defuse_param.splice_bias
444 #else 469 #else
445 #try 470 #try
446 $ref_dict['splice_bias'] 471 $ref_dict['splice_bias']
447 #except 472 #except
448 10 473 10
449 #end try 474 #end try
450 #end if 475 #end if
451 denovo_assembly = #slurp 476 denovo_assembly = #slurp
452 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.denovo_assembly.__str__ != "" 477 #if $defuse_param.settings == "full" and $defuse_param.denovo_assembly.__str__ != ""
453 $refGenomeSource.defuse_param.denovo_assembly 478 $defuse_param.denovo_assembly
454 #else 479 #else
455 #try 480 #try
456 $ref_dict['denovo_assembly'] 481 $ref_dict['denovo_assembly']
457 #except 482 #except
458 no 483 no
459 #end try 484 #end try
460 #end if 485 #end if
461 probability_threshold = #slurp 486 probability_threshold = #slurp
462 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.probability_threshold.__str__ != "" 487 #if $defuse_param.settings == "full" and $defuse_param.probability_threshold.__str__ != ""
463 $refGenomeSource.defuse_param.probability_threshold 488 $defuse_param.probability_threshold
464 #else 489 #else
465 #try 490 #try
466 $ref_dict['probability_threshold'] 491 $ref_dict['probability_threshold']
467 #except 492 #except
468 0.50 493 0.50
469 #end try 494 #end try
470 #end if 495 #end if
471 positive_controls = \$(data_directory)/controls.txt 496 positive_controls = \$(data_directory)/controls.txt
497
498 # Use multiple exon transcripts for stats calculations (yes/no)
499 # should be enabled for very small libraries
500 multi_exon_transcripts_stats = #slurp
501 #if $defuse_param.settings == "full" and $defuse_param.multi_exon_transcripts_stats.__str__ != ""
502 $defuse_param.multi_exon_transcripts_stats
503 #else
504 #try
505 $ref_dict['multi_exon_transcripts_stats']
506 #except
507 no
508 #end try
509 #end if
472 510
473 # Position density when calculating covariance 511 # Position density when calculating covariance
474 covariance_sampling_density = #slurp 512 covariance_sampling_density = #slurp
475 #if $refGenomeSource.defuse_param.settings == "full" and $refGenomeSource.defuse_param.covariance_sampling_density.__str__ != "" 513 #if $defuse_param.settings == "full" and $defuse_param.covariance_sampling_density.__str__ != ""
476 $refGenomeSource.defuse_param.covariance_sampling_density 514 $defuse_param.covariance_sampling_density
477 #else 515 #else
478 #try 516 #try
479 $ref_dict['covariance_sampling_density'] 517 $ref_dict['covariance_sampling_density']
480 #except 518 #except
481 0.01 519 0.01
482 #end try 520 #end try
483 #end if 521 #end if
484 522
523 # Maximum number of alignments for a read pair
524 # Pairs with more alignments are filtered
525 max_paired_alignments = #slurp
526 #if $defuse_param.settings == "full" and $defuse_param.max_paired_alignments.__str__ != ""
527 $defuse_param.max_paired_alignments
528 #else
529 #try
530 $ref_dict['max_paired_alignments']
531 #except
532 10
533 #end try
534 #end if
485 535
486 # Number of reads for each job in split 536 # Number of reads for each job in split
487 reads_per_job = 1000000 537 reads_per_job = #slurp
488 538 #if $defuse_param.settings == "full" and $defuse_param.reads_per_job.__str__ != ""
489 # Number of regions for each breakpoint sequence job in split 539 $defuse_param.reads_per_job
490 regions_per_job = 20 540 #else
541 #try
542 $ref_dict['reads_per_job']
543 #except
544 1000000
545 #end try
546 #end if
491 547
492 #raw 548 #raw
493 # If you have command line 'mail' and wish to be notified 549 # If you have command line 'mail' and wish to be notified
494 # mailto = andrew.mcpherson@gmail.com 550 # mailto = andrew.mcpherson@gmail.com
495 551
496 # Remove temp files 552 # Remove temp files
497 remove_job_files = yes 553 remove_job_files = yes
498 remove_job_temp_files = yes 554 remove_job_temp_files = yes
499 555
500 # Converting to fastq 556 qsub_params = ""
501 # Fastq converter config format 1 for reads stored in separate files for each end 557
502 # data_lane_rexex_N is a perl regex which stores the lane id in $1
503 # data_end_regex_N is a perl regex which stores the end, 1 or 2, in $1
504 # data_compress_regex_N is a perl regex which stores the compression extension in $1
505 # data_convert_N is the associated conversion utility that takes data at stdin and outputs fastq at stdout
506 # Fastq converter config format 2 for reads stored in separate files for each end
507 # data_lane_regex_N is a perl regex which stores the lane id in $1
508 # data_compress_regex_N is a perl regex which stores the compression extension in $1
509 # data_end1_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 1 at stdout
510 # data_end2_converter_N is the associated conversion utility that takes data at stdin and outputs fastq for end 2 at stdout
511
512 data_lane_regex_1 = ^(.+)_[12]_export\.txt.*$
513 data_end_regex_1 = ^.+_([12])_export\.txt.*$
514 data_compress_regex_1 = ^.+_[12]_export\.txt(.*)$
515 data_converter_1 = $(scripts_directory)/fq_all2std.pl export2std
516
517 data_lane_regex_2 = ^(.+)_[12]_concat_qseq\.txt.*$
518 data_end_regex_2 = ^.+_([12])_concat_qseq\.txt.*$
519 data_compress_regex_2 = ^.+_[12]_concat_qseq\.txt(.*)$
520 data_converter_2 = $(scripts_directory)/qseq2fastq.pl
521
522 data_lane_regex_3 = ^(.+)\.bam.*$
523 data_compress_regex_3 = ^.+\.bam(.*)$
524 data_end1_converter_3 = samtools view - | filter_sam_mate.pl 1 | sam_to_fastq.pl
525 data_end2_converter_3 = samtools view - | filter_sam_mate.pl 2 | sam_to_fastq.pl
526
527 data_lane_regex_4 = ^(.+).[12].fastq.*$
528 data_end_regex_4 = ^.+.([12]).fastq.*$
529 data_compress_regex_4 = ^.+.[12].fastq(.*)$
530 data_converter_4 = cat
531 #end raw 558 #end raw
532 559
533 #end if
534 560
535 </configfile> 561 </configfile>
536 <configfile name="shscript"> 562 <configfile name="shscript">
537 #!/bin/bash 563 #!/bin/bash
538 ## define some things for cheetah proccessing 564 ## define some things for cheetah proccessing
586 612
587 ## copy config to output 613 ## copy config to output
588 cp $defuse_config $config_txt 614 cp $defuse_config $config_txt
589 ## make a data_dir and ln -s the input fastq 615 ## make a data_dir and ln -s the input fastq
590 mkdir -p data_dir 616 mkdir -p data_dir
591 ln -s $left_pairendreads data_dir/reads_1.fastq 617 ## ln -s "$left_pairendreads" data_dir/reads_1.fastq
592 ln -s $right_pairendreads data_dir/reads_2.fastq 618 ## ln -s "$right_pairendreads" data_dir/reads_2.fastq
619 cp "$left_pairendreads" data_dir/reads_1.fastq
620 cp "$right_pairendreads" data_dir/reads_2.fastq
593 ## ln to output_dir in from_work_dir 621 ## ln to output_dir in from_work_dir
594 #if $defuse_out.__str__ != 'None': 622 #if $defuse_out.__str__ != 'None':
595 mkdir -p $defuse_out.extra_files_path 623 mkdir -p $defuse_out.dataset.extra_files_path
596 ln -s $defuse_out.extra_files_path output_dir 624 ln -s $defuse_out.dataset.extra_files_path output_dir
597 #else 625 #else
598 mkdir -p output_dir 626 mkdir -p output_dir
599 #end if 627 #end if
600 ## run defuse.pl 628 ## run defuse.pl
601 perl \${DEFUSE_PATH}/scripts/defuse.pl -c $defuse_config -d data_dir -o output_dir -p 8 629 perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS
602 ## copy primary results to output datasets 630 ## copy primary results to output datasets
603 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi 631 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
604 if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi 632 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
605 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi 633 if [ -e output_dir/results.filtered.tsv ]; then cp output_dir/results.filtered.tsv $results_filtered_tsv; fi
606 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi 634 if [ -e output_dir/results.classify.tsv ]; then cp output_dir/results.classify.tsv $results_classify_tsv; fi
635 #if $breakpoints_bam:
636 if [ -e output_dir/results.filtered.tsv ] ${amp}${amp} [ -e output_dir/breakpoints.genome.psl ]
637 then
638 awk "\\$10 ~ /^(`awk '\\$1 ~ /[0-9]+/{print \\$1}' output_dir/results.filtered.tsv | tr '\n' '|'`)\\$/{print \\$0}" output_dir/breakpoints.genome.psl > breakpoints.genome.filtered.psl ${amp}${amp}
639 psl2sam.pl breakpoints.genome.filtered.psl > breakpoints.genome.filtered.sam ${amp}${amp}
640 samtools view -b -T /panfs/roc/rissdb/galaxy/genomes/NCBIM37/defuse/defuse.reference.fa -o breakpoints.genome.filtered.bam breakpoints.genome.filtered.sam ${amp}${amp}
641 samtools sort breakpoints.genome.filtered.bam breakpoints ${amp}${amp}
642 ## samtools index breakpoints.bam
643 cp breakpoints.bam $fusions_bam
644 fi
645 #end if
607 ## create html with links for output_dir 646 ## create html with links for output_dir
608 #if $defuse_out.__str__ != 'None': 647 #if $defuse_out.__str__ != 'None':
609 if [ -e $defuse_out ] 648 if [ -e $defuse_out ]
610 then 649 then
611 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out 650 echo '${lt}html${gt}${lt}head${gt}${lt}title${gt}Defuse Output${lt}/title${gt}${lt}/head${gt}${lt}body${gt}' ${gt} $defuse_out
612 echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out 651 echo '${lt}h2${gt}Defuse Output Files${lt}/h2${gt}${lt}ul${gt}' ${gt}${gt} $defuse_out
613 pushd $defuse_out.extra_files_path 652 pushd $defuse_out.dataset.extra_files_path
614 for f in `find -L . -maxdepth 1 -type f`; 653 for f in `find -L . -maxdepth 1 -type f`;
615 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; 654 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} $defuse_out;
616 done 655 done
617 popd 656 popd
618 echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out 657 echo '${lt}/ul${gt}' ${gt}${gt} $defuse_out
621 #end if 660 #end if
622 ## run get_reads.pl on each cluster 661 ## run get_reads.pl on each cluster
623 #if $fusion_reads.__str__ != 'None': 662 #if $fusion_reads.__str__ != 'None':
624 if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ] 663 if [ -e output_dir/results.filtered.tsv -a -e $fusion_reads ]
625 then 664 then
626 mkdir -p $fusion_reads.extra_files_path 665 mkdir -p $fusion_reads.dataset.extra_files_path
627 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.extra_files_path 666 results2html output_dir/results.filtered.tsv $fusion_reads $fusion_reads.dataset.extra_files_path
628 fi 667 fi
629 #end if 668 #end if
630 </configfile> 669 </configfile>
631 </configfiles> 670 </configfiles>
632 671
751 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 790 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
752 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 - 791 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 -
753 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 - - 792 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 - -
754 793
755 </help> 794 </help>
795 <expand macro="citations"/>
756 </tool> 796 </tool>