Mercurial > repos > dereeper > sniplay3
comparison filterVCFonAnnotations.xml @ 2:15319113c0a5 draft
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author | dereeper |
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date | Thu, 12 Feb 2015 15:54:24 -0500 |
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1:b058193a71d0 | 2:15319113c0a5 |
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1 <tool id="sniplay_filterVCFonAnnotations" name="Filter VCF on Annotations" version="1.0.0"> | |
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 </requirements> | |
10 | |
11 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | |
12 <version_command> | |
13 <!-- | |
14 tool_binary -v | |
15 --> | |
16 </version_command> | |
17 | |
18 <!-- [REQUIRED] The command to execute --> | |
19 <command interpreter="perl"> | |
20 FilterVCFonAnnotations.pl --input $filein --out $fileout | |
21 #if str( $genelist ) != "None": | |
22 --genelist $genelist | |
23 #end if | |
24 #if str( $feature ) != "": | |
25 --feature $feature | |
26 #end if | |
27 #if str( $syn ) != "": | |
28 --syn $syn | |
29 #end if | |
30 </command> | |
31 | |
32 <!-- [REQUIRED] Input files and tool parameters --> | |
33 <inputs> | |
34 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> | |
35 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/> | |
36 <param name="genelist" type="data" format="txt" optional="true" label="Genelist" default="" help="File listing the genes to be filtered, one line per individu/gene"/> | |
37 <param name="feature" type="select" label="Genomic feature" optional="true" help="Filter within genomic feature"> | |
38 <option value="" selected="true">All</option> | |
39 <option value="Exon">Exon</option> | |
40 <option value="INTRON">Intron</option> | |
41 <option value="UTR_5_PRIME">UTR5prime</option> | |
42 <option value="UTR_3_PRIME">UTR3prime</option> | |
43 <option value="DOWNSTREAM">Downstream</option> | |
44 <option value="UPSTREAM">Upstream</option> | |
45 <option value="INTERGENIC">Intergenic</option> | |
46 </param> | |
47 <param name="syn" type="select" label="Synonymous type" optional="true" help="Keep only synonymous, non-synonymous SNP"> | |
48 <option value="" selected="true">All</option> | |
49 <option value="s">Synonymous</option> | |
50 <option value="n">Non-synonymous</option> | |
51 </param> | |
52 </inputs> | |
53 | |
54 <!-- [REQUIRED] Output files --> | |
55 <outputs> | |
56 <data name="fileout" type="data" format="vcf" label="${fileout_label}.vcf" /> | |
57 </outputs> | |
58 | |
59 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
60 <stdio> | |
61 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
62 <exit_code range="1:" level="fatal" /> | |
63 </stdio> | |
64 | |
65 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
66 <tests> | |
67 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
68 <test> | |
69 <param name="filein" value="sample.vcf" /> | |
70 <param name="genelist" value="accession.txt" /> | |
71 <param name="feature" value="INTRON" /> | |
72 <output name="fileout" file="result.vcf" /> | |
73 </test> | |
74 </tests> | |
75 | |
76 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
77 <help> | |
78 | |
79 .. class:: infomark | |
80 | |
81 **Authors** | |
82 | |
83 --------------------------------------------------- | |
84 | |
85 .. class:: infomark | |
86 | |
87 **Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep. | |
88 | |
89 --------------------------------------------------- | |
90 | |
91 ====================== | |
92 Filter And Convert VCF | |
93 ====================== | |
94 | |
95 ----------- | |
96 Description | |
97 ----------- | |
98 | |
99 Filter VCF file and convert in Fasta, Hapmap and PED | |
100 | |
101 ----------------- | |
102 Workflow position | |
103 ----------------- | |
104 | |
105 **Upstream tools** | |
106 | |
107 =========== ========================== ======= | |
108 Name output file(s) format | |
109 =========== ========================== ======= | |
110 =========== ========================== ======= | |
111 | |
112 | |
113 **Downstream tools** | |
114 | |
115 =========== ========================== ======= | |
116 Name output file(s) format | |
117 =========== ========================== ======= | |
118 =========== ========================== ======= | |
119 | |
120 | |
121 ---------- | |
122 Input file | |
123 ---------- | |
124 | |
125 VCF file | |
126 VCF file with all SNPs | |
127 | |
128 Genelist | |
129 File listing the genes or individuals to be filtered. Gene_id or accesion number can be put in a file, one line per individual | |
130 | |
131 | |
132 ---------- | |
133 Parameters | |
134 ---------- | |
135 | |
136 Output file name | |
137 Prefix for the output VCF file | |
138 | |
139 Genomic feature | |
140 Filter on genomic feature : Exon,INTRON,UTR_3_PRIME,UTR_5_PRIME,DOWNSTREAM,UPSTREAM or INTERGENIC | |
141 | |
142 Synonymous type | |
143 Keep only synonymous, non-synonymous. | |
144 | |
145 | |
146 ------------ | |
147 Output files | |
148 ------------ | |
149 | |
150 VCF file | |
151 VCF file filtered | |
152 | |
153 --------------------------------------------------- | |
154 | |
155 --------------- | |
156 Working example | |
157 --------------- | |
158 | |
159 Input files | |
160 =========== | |
161 | |
162 VCF file | |
163 --------- | |
164 | |
165 :: | |
166 | |
167 #fileformat=VCFv4.1 | |
168 #FILTER=<ID=LowQual,Description="Low quality"> | |
169 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
170 [...] | |
171 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 | |
172 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 | |
173 | |
174 Genelist | |
175 --------- | |
176 | |
177 :: | |
178 | |
179 Cc01g00020 | |
180 Cc01g00010 | |
181 | |
182 Parameters | |
183 ========== | |
184 | |
185 Output name -> filtered_genelist_intron | |
186 | |
187 Genomic feature -> Intron | |
188 | |
189 Output files | |
190 ============ | |
191 | |
192 filtered_genelist_intron.vcf | |
193 ---------------------------- | |
194 | |
195 :: | |
196 | |
197 #fileformat=VCFv4.1 | |
198 #FILTER=<ID=LowQual,Description="Low quality"> | |
199 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
200 [...] | |
201 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 | |
202 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 | |
203 | |
204 | |
205 </help> | |
206 | |
207 </tool> |