Mercurial > repos > dereeper > sniplay3
comparison vcfToolsStats.xml @ 1:b058193a71d0 draft
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author | dereeper |
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date | Thu, 12 Feb 2015 15:41:00 -0500 |
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0:9dec9f724a50 | 1:b058193a71d0 |
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1 <tool id="sniplay_vcftoolsstats" name="VCF tools Stats" 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 <requirement type="package" version="0.1.13">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 vcfToolsStats.sh $filein $fileout_label $fileout_annot $fileout_het $fileout_imiss $fileout_sum $filelog | |
22 </command> | |
23 | |
24 <!-- [REQUIRED] Input files and tool parameters --> | |
25 <inputs> | |
26 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> | |
27 <param name="fileout_label" type="text" value="vcf_stats" optional="false" label="Output file basename"/> | |
28 </inputs> | |
29 | |
30 <!-- [REQUIRED] Output files --> | |
31 <outputs> | |
32 <data name="fileout_annot" format="txt" label="${fileout_label}.annotation" /> | |
33 <data name="fileout_het" format="txt" label="${fileout_label}.het" /> | |
34 <data name="fileout_imiss" format="txt" label="${fileout_label}.imiss" /> | |
35 <data name="fileout_sum" format="txt" label="${fileout_label}.TsTv.summary" /> | |
36 <data name="filelog" format="txt" label="${fileout_label}.log" /> | |
37 </outputs> | |
38 | |
39 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
40 <stdio> | |
41 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
42 <exit_code range="1:" level="fatal" /> | |
43 </stdio> | |
44 | |
45 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
46 <tests> | |
47 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
48 <test> | |
49 <param name="filein" value="sample.vcf" /> | |
50 <output name="fileout_annot" file="result.annotation" /> | |
51 <output name="fileout_het" file="result.het" /> | |
52 <output name="fileout_imiss" file="result.imiss" /> | |
53 <output name="fileout_sum" file="result.TsTv.summary" /> | |
54 <output name="filelog" file="result.log" /> | |
55 </test> | |
56 </tests> | |
57 | |
58 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
59 <help> | |
60 | |
61 .. class:: infomark | |
62 | |
63 **Authors** | |
64 | |
65 --------------------------------------------------- | |
66 | |
67 .. class:: infomark | |
68 | |
69 **Please cite** If you use this tool, please cite Dereeper et al. 2015 in prep. | |
70 | |
71 --------------------------------------------------- | |
72 | |
73 ================ | |
74 VCF tools filter | |
75 ================ | |
76 | |
77 ----------- | |
78 Description | |
79 ----------- | |
80 | |
81 Compute statistics on VCF file | |
82 | |
83 ----------------- | |
84 Workflow position | |
85 ----------------- | |
86 | |
87 **Upstream tools** | |
88 | |
89 =========== ========================== ======= | |
90 Name output file(s) format | |
91 =========== ========================== ======= | |
92 =========== ========================== ======= | |
93 | |
94 | |
95 **Downstream tools** | |
96 | |
97 =========== ========================== ======= | |
98 Name output file(s) format | |
99 =========== ========================== ======= | |
100 =========== ========================== ======= | |
101 | |
102 | |
103 ---------- | |
104 Input file | |
105 ---------- | |
106 | |
107 VCF file | |
108 VCF file with all SNPs | |
109 | |
110 ---------- | |
111 Parameters | |
112 ---------- | |
113 | |
114 Output file basename | |
115 Prefix for the output VCF file | |
116 | |
117 ------------ | |
118 Output files | |
119 ------------ | |
120 | |
121 .annotation file | |
122 Statistics on annotation/location along genome | |
123 | |
124 .het file | |
125 Statistics on heterozygosity of the individuals | |
126 | |
127 .imiss | |
128 Statistics on missing data of the inidividuals | |
129 .TsTv.summary | |
130 Statistics on mutation types and transition/transvertion number | |
131 | |
132 .log file | |
133 | |
134 --------------------------------------------------- | |
135 | |
136 --------------- | |
137 Working example | |
138 --------------- | |
139 | |
140 Input files | |
141 =========== | |
142 | |
143 VCF file | |
144 --------- | |
145 | |
146 :: | |
147 | |
148 #fileformat=VCFv4.1 | |
149 #FILTER=<ID=LowQual,Description="Low quality"> | |
150 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
151 [...] | |
152 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 | |
153 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 | |
154 | |
155 | |
156 Parameters | |
157 ========== | |
158 | |
159 Output name -> vcf_stat | |
160 | |
161 | |
162 Output files | |
163 ============ | |
164 | |
165 .annotation file | |
166 ---------------- | |
167 | |
168 :: | |
169 | |
170 Genic 4489 | |
171 Intergenic 466 | |
172 ======== | |
173 Intron 960 | |
174 Exon 3248 | |
175 UTR 281 | |
176 ======== | |
177 Non-syn 226 | |
178 Synonym 3022 | |
179 | |
180 .het file | |
181 --------- | |
182 | |
183 :: | |
184 | |
185 INDV O(HOM) E(HOM) N_SITES F | |
186 CATB1 0 0.0 3616 0.00000 | |
187 | |
188 .imiss file | |
189 ----------- | |
190 | |
191 :: | |
192 | |
193 INDV N_DATA N_GENOTYPES_FILTERED N_MISS F_MISS | |
194 CATB1 4813 0 0 0 | |
195 | |
196 .TsTv.summary file | |
197 ------------------ | |
198 | |
199 :: | |
200 | |
201 MODEL COUNT | |
202 AC 371 | |
203 AG 1467 | |
204 AT 562 | |
205 CG 330 | |
206 CT 1659 | |
207 GT 397 | |
208 Ts 3126 | |
209 Tv 1660 | |
210 | |
211 | |
212 </help> | |
213 | |
214 </tool> |