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comparison VCFToolsStats/vcfToolsStats.xml @ 21:50bd37c444ac draft

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author dereeper
date Mon, 23 Mar 2015 05:35:48 -0400
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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> Various statistics from VCF using VCFtools</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=&lt;ID=LowQual,Description="Low quality">
150 #FORMAT=&lt;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>