Mercurial > repos > fcaramia > contra
comparison contra.xml @ 23:2770f49cb0dc
re-uploading contra
author | Franco Caramia <franco.caramia@petermac.org> |
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date | Tue, 20 May 2014 09:59:00 +1000 |
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children | c361b3fb806e |
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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 |