Mercurial > repos > gandres > vcftools_filter_stats_diversity
comparison vcftools_main/VCFToolFilter/vcfToolsFilter.xml @ 0:3b1436a9a6e5 draft
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author | gandres |
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date | Thu, 02 Jul 2015 05:21:40 -0400 |
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children | 0f67ed444d47 |
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1 <tool id="sniplay_vcftoolsfilter" name="VCFtools Filter" version="1.1.1"> | |
2 | |
3 <!-- [REQUIRED] Tool description displayed after the tool name --> | |
4 <description> </description> | |
5 | |
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> | |
7 <requirements> | |
8 <requirement type="binary">perl</requirement> | |
9 <requirement type="package" version="0.1.12b">vcftools</requirement> | |
10 </requirements> | |
11 | |
12 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | |
13 <version_command> | |
14 <!-- | |
15 tool_binary -v | |
16 --> | |
17 </version_command> | |
18 | |
19 <!-- [REQUIRED] The command to execute --> | |
20 <command interpreter="perl"> | |
21 vcfToolsFilter.sh $filein $fileout_label $fileout $filelog $export $frequency $max_freq $allow_missing $nb_alleles_min $nb_alleles_max $type_p $bound_start $bound_end | |
22 #if str( $samples ) == "": | |
23 'None' | |
24 #else | |
25 $samples | |
26 #end if | |
27 #if str( $chromosomes ) == "": | |
28 'None' | |
29 #else | |
30 $chromosomes | |
31 #end if | |
32 #if str( $export ) == "plink": | |
33 $fileout_map | |
34 #else | |
35 '' | |
36 #end if | |
37 </command> | |
38 | |
39 <!-- [REQUIRED] Input files and tool parameters --> | |
40 <inputs> | |
41 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> | |
42 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file basename"/> | |
43 <param name="samples" type="text" optional="true" label="Samples" help="Samples to be analyzed. Comma separated list"> | |
44 <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator> | |
45 </param> | |
46 <param name="chromosomes" type="text" optional="true" label="Chromosomes" help="Chromosomes to be analyzed. Comma separated list"> | |
47 <validator type="regex" message="Please enter a comma separated list.">^\w+(,\w+)*$</validator> | |
48 </param> | |
49 <param name="export" type="select" label="Output format" > | |
50 <option value="VCF" selected="true">VCF</option> | |
51 <option value="freq">freq</option> | |
52 <option value="plink">plink</option> | |
53 </param> | |
54 <param name="frequency" type="float" value="0.001" label="Minimum MAF." help="Minimum frequency." /> | |
55 <param name="max_freq" type="float" value="0.5" label="Maximum MAF." help="Maximum frequency." /> | |
56 <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." /> | |
57 <param name="nb_alleles_min" type="integer" value="2" label="Minimum number of alleles" help="Minimum accepted number of alleles." min="2" max="4" /> | |
58 <param name="nb_alleles_max" type="integer" value="2" label="Maximum number of alleles" help="Maximum accepted number of alleles." min="2" max="4" /> | |
59 <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." > | |
60 <option value="ALL" selected="true">All</option> | |
61 <option value="SNP">SNP</option> | |
62 <option value="INDEL">Indel</option> | |
63 </param> | |
64 <param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." /> | |
65 <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." /> | |
66 </inputs> | |
67 | |
68 <!-- [REQUIRED] Output files --> | |
69 <outputs> | |
70 <data name="fileout" format="vcf" label="${fileout_label}.#if str($export)=='plink' then 'ped' else '' # #if str($export)=='freq' then 'frq' else '' # #if str($export)=='VCF' then 'vcf' else '' #" > | |
71 <change_format> | |
72 <when input="export" value="freq" format="tabular" /> | |
73 <when input="export" value="plink" format="txt" /> | |
74 </change_format> | |
75 </data> | |
76 <data name="fileout_map" format="txt" label="${fileout_label}.map"> | |
77 <filter>(export == 'plink')</filter> | |
78 </data> | |
79 <data name="filelog" format="txt" label="${fileout_label}.log" /> | |
80 </outputs> | |
81 | |
82 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
83 <stdio> | |
84 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
85 <exit_code range="1:" level="fatal" /> | |
86 </stdio> | |
87 | |
88 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
89 <tests> | |
90 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
91 <test> | |
92 <param name="filein" value="sample.vcf" /> | |
93 <param name="chromosomes" value="chr1" /> | |
94 <param name="export" value="VCF" /> | |
95 <param name="frequency" value="0.001" /> | |
96 <param name="max_freq" value="0.5" /> | |
97 <param name="allow_missing" value="1" /> | |
98 <param name="nb_alleles_min" value="2" /> | |
99 <param name="nb_alleles_max" value="4" /> | |
100 <param name="type_p" value="ALL" /> | |
101 <param name="bound_start" value="1" /> | |
102 <param name="bound_end" value="100000000" /> | |
103 <output name="fileout" file="result.vcf" /> | |
104 <output name="filelog" file="result.log" /> | |
105 </test> | |
106 </tests> | |
107 | |
108 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
109 <help> | |
110 | |
111 .. class:: infomark | |
112 | |
113 **Authors** Dereeper Alexis | |
114 | |
115 | Dereeper et al. 2015 in prep. | |
116 | |
117 | |
118 .. class:: infomark | |
119 | |
120 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. | |
121 | |
122 .. class:: infomark | |
123 | |
124 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr | |
125 | |
126 --------------------------------------------------- | |
127 | |
128 | |
129 | |
130 ================ | |
131 VCF tools filter | |
132 ================ | |
133 | |
134 ----------- | |
135 Description | |
136 ----------- | |
137 | |
138 Filter VCF file | |
139 | |
140 ----------------- | |
141 Workflow position | |
142 ----------------- | |
143 | |
144 **Upstream tools** | |
145 | |
146 =========== ========================== ======= | |
147 Name output file(s) format | |
148 =========== ========================== ======= | |
149 =========== ========================== ======= | |
150 | |
151 | |
152 **Downstream tools** | |
153 | |
154 =========== ========================== ======= | |
155 Name output file(s) format | |
156 =========== ========================== ======= | |
157 =========== ========================== ======= | |
158 | |
159 | |
160 ---------- | |
161 Input file | |
162 ---------- | |
163 | |
164 VCF file | |
165 VCF file with all SNPs | |
166 | |
167 ---------- | |
168 Parameters | |
169 ---------- | |
170 | |
171 Output file basename | |
172 Prefix for the output VCF file | |
173 | |
174 Samples | |
175 Samples to be analyzed. Comma separated list | |
176 | |
177 Chromosomes | |
178 Chromosomes to be analyzed. Comma separated list | |
179 | |
180 Output format | |
181 VCF/freq/plink | |
182 | |
183 Minimum MAF | |
184 Minimum frequency | |
185 | |
186 Maximum MAF | |
187 Maximum frequency | |
188 | |
189 Missing data proportion | |
190 Allowed missing data proportion per site. Must be comprised between 0 and 1. | |
191 | |
192 Number of alleles | |
193 Accepted number of alleles min and max. | |
194 | |
195 Polymorphisms | |
196 Type of polymorphisms to keep (ALL/SNP/INDEL). | |
197 Bounds | |
198 Lower bound and upper bound for a range of sites to be processed. | |
199 | |
200 ------------ | |
201 Output files | |
202 ------------ | |
203 | |
204 VCF file | |
205 VCF file filtered | |
206 | |
207 Log file | |
208 | |
209 --------------------------------------------------- | |
210 | |
211 --------------- | |
212 Working example | |
213 --------------- | |
214 | |
215 Input files | |
216 =========== | |
217 | |
218 VCF file | |
219 --------- | |
220 | |
221 :: | |
222 | |
223 #fileformat=VCFv4.1 | |
224 #FILTER=<ID=LowQual,Description="Low quality"> | |
225 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
226 [...] | |
227 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 | |
228 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 | |
229 | |
230 | |
231 Parameters | |
232 ========== | |
233 | |
234 Output name -> filtered_chr1 | |
235 | |
236 Chromosomes -> chr1 | |
237 | |
238 Output format -> VCF | |
239 | |
240 Minimum MAF -> 0.001 | |
241 | |
242 Maximum MAF -> 0.5 | |
243 | |
244 Missing data proportion -> 1 | |
245 | |
246 Number of alleles min -> 2 | |
247 | |
248 Number of alleles max -> 4 | |
249 | |
250 Polymorphisms -> All | |
251 | |
252 Lower bound -> 1 | |
253 | |
254 Upper bound -> 100000000 | |
255 | |
256 | |
257 Output files | |
258 ============ | |
259 | |
260 filtered_genelist_intron.vcf | |
261 ---------------------------- | |
262 | |
263 :: | |
264 | |
265 #fileformat=VCFv4.1 | |
266 #FILTER=<ID=LowQual,Description="Low quality"> | |
267 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
268 [...] | |
269 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 | |
270 chr1 5059 . C G 146.84 . AC=2;AF=1.00;AN=2;DP=8;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=24.14;MQ0=1;QD=18.35;EFF=INTRON(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,8:8:18:175,18,0 | |
271 | |
272 | |
273 </help> | |
274 | |
275 </tool> |