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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit ccfbe9e77653393089624d308873496d1d7e32a7
author drosofff
date Wed, 07 Dec 2016 12:26:19 -0500
parents 083280e54e71
children d2202509b46c
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4:083280e54e71 5:57b7aaa3347e
1 <tool id="lumpy" name="lumpy-sv" version="0.2"> 1 <tool id="lumpy" name="lumpy-sv" version="0.2">
2 <description>find structural variants</description> 2 <description>find structural variants</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.12">lumpy-sv</requirement> 4 <requirement type="package" version="0.2.12">lumpy-sv</requirement>
5 <requirement type="package" version="1.3.1">samtools</requirement> 5 <requirement type="package" version="1.3.1">samtools</requirement>
6 <requirement type="package" version="1.11.2">numpy</requirement> 6 <requirement type="package" version="1.11.2=py27">numpy</requirement>
7 </requirements> 7 </requirements>
8 <stdio> 8 <stdio>
9 <exit_code range="1:" level="fatal" description="Tool exception" /> 9 <exit_code range="1:" level="fatal" description="Tool exception" />
10 </stdio> 10 </stdio>
11 <version_command>lumpy --version</version_command> 11 <version_command>lumpy --version</version_command>
12 <command><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 #if $analysis_type.analysis_type_list == "one_sample": 13 #if $analysis_type.analysis_type_list == "one_sample":
14 ln -f -s $analysis_type.input_file input.bam && 14 ln -f -s '$analysis_type.input_file' input.bam &&
15 #else: 15 #else:
16 ln -f -s $analysis_type.input_file input.A.bam && 16 ln -f -s '$analysis_type.input_file' input.A.bam &&
17 ln -f -s $analysis_type.input_fileB input.B.bam && 17 ln -f -s '$analysis_type.input_fileB' input.B.bam &&
18 #end if 18 #end if
19 19
20 #if $analysis_type.analysis_type_list == "one_sample": 20 #if $analysis_type.analysis_type_list == "one_sample":
21 21
22 #if $seq_method.seq_method_list == "paired-end": 22 #if $seq_method.seq_method_list == "paired-end":
144 </conditional> 144 </conditional>
145 145
146 </inputs> 146 </inputs>
147 147
148 <outputs> 148 <outputs>
149 <data format="tabular" name="histogram" label="Lumpy on ${analysis_type.input_file.element_identifier}: Fragment size distribution"> 149 <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution">
150 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 150 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
151 </data> 151 </data>
152 <data format="tabular" name="histogramB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Fragment size distribution"> 152 <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution">
153 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 153 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
154 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 154 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
155 </data> 155 </data>
156 <data format="bam" name="splits" label="Lumpy on ${analysis_type.input_file.element_identifier}: Split Reads (Bam format)"/> 156 <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)"/>
157 <data format="bam" name="splitsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Split Reads (Bam format)"> 157 <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)">
158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 158 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
159 </data> 159 </data>
160 <data format="bam" name="discordants" label="Lumpy on ${analysis_type.input_file.element_identifier}: Discordant Pairs (Bam format)"> 160 <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)">
161 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 161 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
162 </data> 162 </data>
163 <data format="bam" name="discordantsB" label="Lumpy on ${analysis_type.input_fileB.element_identifier}: Discordant Pairs (Bam format)"> 163 <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)">
164 <filter>seq_method['seq_method_list'] == "paired-end"</filter> 164 <filter>seq_method['seq_method_list'] == "paired-end"</filter>
165 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> 165 <filter>analysis_type['analysis_type_list'] == "two_sample"</filter>
166 </data> 166 </data>
167 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/> 167 <data format="vcf" name="vcf_call" label="Lumpy Variant Calling (vcf format)"/>
168 </outputs> 168 </outputs>
215 Author: Ryan Layer (rl6sf@virginia.edu) 215 Author: Ryan Layer (rl6sf@virginia.edu)
216 216
217 Summary: Find structural variations in various signals. 217 Summary: Find structural variations in various signals.
218 218
219 Options:: 219 Options::
220 <![CDATA[
220 221
221 -g Genome file (defines chromosome order) 222 -g Genome file (defines chromosome order)
222 -e Show evidence for each call 223 -e Show evidence for each call
223 -w File read windows size (default 1000000) 224 -w File read windows size (default 1000000)
224 -mw minimum weight for a call 225 -mw minimum weight for a call
226 -tt trim threshold 227 -tt trim threshold
227 -x exclude file bed file 228 -x exclude file bed file
228 -t temp file prefix, must be to a writeable directory 229 -t temp file prefix, must be to a writeable directory
229 -P output probability curve for each variant 230 -P output probability curve for each variant
230 -b output BEDPE instead of VCF 231 -b output BEDPE instead of VCF
231 -sr bam_file:&lt;file name&gt;, 232 -sr bam_file:<file name>,
232 id:&lt;sample name&gt;, 233 id:<sample name>,
233 back_distance:&lt;distance&gt;, 234 back_distance:<distance>,
234 min_mapping_threshold:&lt;mapping quality&gt;, 235 min_mapping_threshold:<mapping quality>,
235 weight:&lt;sample weight&gt;, 236 weight:<sample weight>,
236 min_clip:&lt;minimum clip length&gt;, 237 min_clip:<minimum clip length>,
237 read_group:&lt;string&gt; 238 read_group:<string>
238 239
239 -pe bam_file:&lt;file name&gt;, 240 -pe bam_file:<file name>,
240 id:&lt;sample name&gt;, 241 id:<sample name>,
241 histo_file:&lt;file name&gt;, 242 histo_file:<file name>,
242 mean:&lt;value&gt;, 243 mean:<value>,
243 stdev:&lt;value&gt;, 244 stdev:<value>,
244 read_length:&lt;length&gt;, 245 read_length:<length>,
245 min_non_overlap:&lt;length&gt;, 246 min_non_overlap:<length>,
246 discordant_z:&lt;z value&gt;, 247 discordant_z:<z value>,
247 back_distance:&lt;distance&gt;, 248 back_distance:<distance>,
248 min_mapping_threshold:&lt;mapping quality&gt;, 249 min_mapping_threshold:<mapping quality>,
249 weight:&lt;sample weight&gt;, 250 weight:<sample weight>,
250 read_group:&lt;string&gt; 251 read_group:<string>
251 252
252 -bedpe bedpe_file:&lt;bedpe file&gt;, 253 -bedpe bedpe_file:<bedpe file>,
253 id:&lt;sample name&gt;, 254 id:<sample name>,
254 weight:&lt;sample weight&gt; 255 weight:<sample weight>
255 256 ]]>
256 </help> 257 </help>
257 258
258 <citations> 259 <citations>
259 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> 260 <citation type="doi">10.1186/gb-2014-15-6-r84</citation>
260 </citations> 261 </citations>