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re-uploading contra
author Franco Caramia <franco.caramia@petermac.org>
date Tue, 20 May 2014 09:59:00 +1000
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children c361b3fb806e
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22:e8a98923965e 23:2770f49cb0dc
1 <tool id="contra_tool" name="Contra Copy number analysis" version="1.0.0">
2 <description>: Copy Number Analysis for Targeted Resequencing</description>
3 <requirements>
4 <requirement type="package" version="2.17.0">bedtools</requirement>
5 <requirement type="package" name="samtools" version="0.1.18">samtools</requirement>
6 <requirement type="package" name="contra" version="2.0.4">contra</requirement>
7 </requirements>
8 <command interpreter="perl">
9
10 contra_wrapper.pl
11
12 ##Ref Genome
13 #if $genomeSource.refGenomeSource == "history":
14 "PLAYEROPTION::-f=${genomeSource.ownFile}"
15 #else:
16 ##use precomputed indexes
17 "PLAYEROPTION::-f=${genomeSource.indices.fields.path}"
18 #end if
19
20 ##Required files
21 "PLAYEROPTION::-t=$target_file"
22 "PLAYEROPTION::-s=$alignment_file"
23 #if $controlSource.refControlSource == "history":
24 "PLAYEROPTION::-c=${controlSource.control_file}"
25 #else:
26 ##use precomputed indexes
27 "PLAYEROPTION::-c=${controlSource.indices.fields.path}"
28 #end if
29
30 ##Optional parameter
31
32 #if $option.option == "modify_parameters":
33
34 "PLAYEROPTION::--numBin=$option.numBin"
35 "PLAYEROPTION::--minReadDepth=$option.minReadDepth"
36 "PLAYEROPTION::--minNBases=$option.minNbases"
37
38 #if str($option.sam) == "true":
39 "PLAYEROPTION::--sam"
40 #end if
41
42 #if str($option.bed) == "true":
43 "PLAYEROPTION::--bed"
44 #end if
45
46 "PLAYEROPTION::--pval=$option.pval"
47 "PLAYEROPTION::--sampleName=$option.sampleName"
48
49 #if str($option.nomultimapped) == "true":
50 "PLAYEROPTION::--nomultimapped"
51 #end if
52
53 #if str($option.plot) == "true":
54 "PLAYEROPTION::--plot"
55 #end if
56
57 "PLAYEROPTION::--minExon=$option.minExon"
58 "PLAYEROPTION::--minControlRdForCall=$option.minControlRdForCall"
59 "PLAYEROPTION::--minTestRdForCall=$option.minTestRdForCall"
60 "PLAYEROPTION::--minAvgForCall=$option.minAvgForCall"
61 "PLAYEROPTION::--maxRegionSize=$option.maxRegionSize"
62 "PLAYEROPTION::--targetRegionSize=$option.targetRegionSize"
63
64 #if str($option.largedeletion) == "true":
65 "PLAYEROPTION::--largedeletion"
66 #end if
67
68 "PLAYEROPTION::--smallSegment=$option.smallSegment"
69 "PLAYEROPTION::--targetRegionSize=$option.targetRegionSize"
70 "PLAYEROPTION::--largeSegment=$option.largeSegment"
71 "PLAYEROPTION::--lrCallStart=$option.lrCallStart"
72 "PLAYEROPTION::--lrCallEnd=$option.lrCallEnd"
73 "PLAYEROPTION::--passSize=$option.passSize"
74 #end if
75
76 ##File to generate the bam list
77 CONTRAOUTPUT::$html_file
78 CONTRADIR::$html_file.files_path
79
80 </command>
81 <inputs>
82
83 <conditional name="genomeSource">
84 <param name="refGenomeSource" type="select" label="Will you select a reference from your history or use a built-in fasta file?">
85 <option value="indexed">Use a built-in index</option>
86 <option value="history">Use one from the history</option>
87 </param>
88 <when value="indexed">
89 <param name="indices" type="select" label="Select a reference genome">
90 <options from_data_table="all_fasta">
91 <filter type="sort_by" column="2" />
92 <validator type="no_options" message="No indexes are available" />
93 </options>
94 </param>
95 </when>
96 <when value="history">
97 <param name="ownFile" type="data" format="fasta" label="Select a reference from history" />
98 </when>
99 </conditional>
100
101 <param name="target_file" type="data" format="bed" help="" optional="false" />
102 <param name="alignment_file" type="data" format="bam,sam" help="" optional="false" />
103
104
105 <conditional name="controlSource">
106 <param name="refControlSource" type="select" label="Will you select a reference from your history or use a built-in control file?">
107 <option value="indexed">Use a built-in control</option>
108 <option value="history">Use one from the history</option>
109 </param>
110 <when value="indexed">
111 <param name="indices" type="select" label="Select a baseline control">
112 <options from_data_table="baseline_files">
113 <filter type="sort_by" column="2" />
114 <validator type="no_options" message="No files available" />
115 </options>
116 </param>
117 </when>
118 <when value="history">
119 <param name="control_file" type="data" format="bam,sam,bed,tabular" help="" optional="false" />
120 </when>
121 </conditional>
122
123 <conditional name="option">
124 <param name="option" type="select" label="Optional Parameters" help="" optional="true">
125 <option value="default_parameters" selected="true">Default Parameters</option>
126 <option value="modify_parameters">Modify Parameters</option>
127 </param>
128 <when value="modify_parameters">
129 <param name="numBin" type="integer" value="20" optional="true" />
130 <param name="minReadDepth" type="integer" value="10" optional="true" />
131 <param name="minNbases" type="integer" value="10" optional="true" />
132 <param name="sam" type="select" label="sam" help="" optional="true">
133 <option value="true" >true</option>
134 <option value="false" selected="true">false</option>
135 </param>
136 <param name="bed" type="select" label="bed" help="" optional="true">
137 <option value="true" >true</option>
138 <option value="false" selected="true">false</option>
139 </param>
140 <param name="pval" type="float" value="0.05" optional="true" />
141 <param name="sampleName" value="Contra_Output" type="text" optional="true" />
142 <param name="nomultimapped" type="select" label="no multimapped" help="" optional="true">
143 <option value="true" >true</option>
144 <option value="false" selected="true">false</option>
145 </param>
146 <param name="plot" type="select" label="plot" help="" optional="true">
147 <option value="true" >true</option>
148 <option value="false" selected="true">false</option>
149 </param>
150 <param name="minExon" type="integer" value="2000" optional="true" />
151 <param name="minControlRdForCall" type="integer" value="5" optional="true" />
152 <param name="minTestRdForCall" type="integer" value="0" optional="true" />
153 <param name="minAvgForCall" type="integer" value="20" optional="true" />
154 <param name="maxRegionSize" type="integer" value="0" optional="true" />
155 <param name="targetRegionSize" type="integer" value="200" optional="true" />
156 <param name="largedeletion" type="select" label="large deletion" help="" optional="true">
157 <option value="true" >true</option>
158 <option value="false" selected="true">false</option>
159 </param>
160
161 <param name="smallSegment" type="integer" value="1" optional="true" />
162 <param name="largeSegment" type="integer" value="25" optional="true" />
163 <param name="lrCallStart" type="float" value="-0.3" optional="true" />
164 <param name="lrCallEnd" type="float" value="0.3" optional="true" />
165 <param name="passSize" type="float" value="0.5" optional="true" />
166
167 </when>
168 </conditional>
169 </inputs>
170 <outputs>
171 <data name="html_file" format="html" label="Contra Output" />
172 </outputs>
173 <help>
174 |
175
176
177 **Reference**
178 http://contra-cnv.sourceforge.net/
179
180 -----
181
182 **What it does**
183
184 CONTRA is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. CONTRA calls copy number gains and losses for each target region with key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. It takes standard alignment formats (BAM/SAM) and output in variant call format (VCF 4.0) for easy integration with other next generation sequencing analysis package.
185
186
187 -----
188
189 **Required Parameters**
190
191 ::
192
193 -t, --target Target region definition file [BED format]
194
195 -s, --test Alignment file for the test sample [BAM/SAM]
196
197 -c, --control Alignment file for the control sample
198 [BAM/SAM/BED – baseline file]
199
200 --bed **option has to be supplied for control
201 with baseline file.**
202
203 -f, --fasta Reference genome [FASTA]
204
205 -o, --outFolder the folder name (and its path) to store the output
206 of the analysis (this new folder will be created –
207 error message occur if the folder exists)
208
209 -----
210
211 **Optional Parameters**
212
213 ::
214
215 --numBin Numbers of bins to group the regions. User can
216 specify multiple experiments with different numbers
217 of bins (comma separated). [Default: 20]
218
219 --minReadDepth The threshold for minimum read depth for each bases
220 (see Step 2 in CONTRA workflow) [Default: 10]
221
222 --minNBases The threshold for minimum number of bases for each
223 target regions (see Step 2 in CONTRA workflow)
224 [Default: 10]
225
226 --sam If the specified test and control samples are in
227 SAM format. [Default: False] (It will always take
228 BAM samples as default)
229
230 --bed If specified, control will be a baseline file in
231 BED format. [Default: False]
232 Please refer to the Baseline Script section for
233 instruction how to create baseline files from set
234 of BAMfiles. A set of baseline files from different
235 platform have also been provided in the CONTRA
236 download page.
237
238 --pval The p-value threshold for filtering. Based on Adjusted
239 P-Values. Only regions that pass this threshold will
240 be included in the VCF file. [Default: 0.05]
241
242 --sampleName The name to be appended to the front of the default output
243 name. By default, there will be nothing appended.
244
245 --nomultimapped The option to remove multi-mapped reads
246 (using SAMtools with mapping quality > 0).
247 [default: FALSE]
248
249 -p, --plot If specified, plots of log-ratio distribution for each
250 bin will be included in the output folder [default: FALSE]
251
252 --minExon Minimum number of exons in one bin (if less than this number
253 , bin that contains small number of exons will be merged to
254 the adjacent bins) [Default : 2000]
255
256 --minControlRdForCall Minimum Control ReadDepth for call [Default: 5]
257
258 --minTestRdForCall Minimum Test ReadDepth for call [Default: 0]
259
260 --minAvgForCall Minimum average coverage for call [Default: 20]
261
262 --maxRegionSize Maximum region size in target region (for breaking
263 large regions into smaller regions. By default,
264 maxRegionSize=0 means no breakdown). [Default : 0]
265
266 --targetRegionSize Target region size for breakdown (if maxRegionSize
267 is non-zero) [Default: 200]
268
269 -l, --largeDeletion If specified, CONTRA will run large deletion analysis (CBS).
270 User must have DNAcopy R-library installed to run the
271 analysis. [False]
272
273 --smallSegment CBS segment size for calling large variations [Default : 1]
274
275 --largeSegment CBS segment size for calling large variations [Default : 25]
276
277 --lrCallStart Log ratios start range that will be used to call CNV
278 [Default : -0.3]
279
280 --lrCallEnd Log ratios end range that will be used to call CNV
281 [Default : 0.3]
282
283 --passSize Size of exons that passed the p-value threshold compare
284 to the original exons size [Default: 0.5]
285 </help>
286 </tool>
287
288