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comparison VCF2Hapmap/vcf2FastaAndHapmap.xml @ 3:345f88a8f483 draft

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author dereeper
date Fri, 10 Jul 2015 10:38:43 -0400
parents 420b57c3c185
children 10627af23f10
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2:feb40a9a8eae 3:345f88a8f483
1 <tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="1.1.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> Convert VCF to Hapmap </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="bash">
20 vcf2FastaAndHapmap.sh $filein $fileout_label $fileout $optional.file_opt
21 #if str( $optional.file_opt ) != "none":
22 $fileout_seq $fileout_fa1 $filefasta
23 #if str( $optional.file_opt ) == "fasta_gff":
24 $filegff
25 #end if
26 #end if
27 </command>
28
29 <!-- [REQUIRED] Input files and tool parameters -->
30 <inputs>
31 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
32 <param name="fileout_label" type="text" value="input" optional="false" label="Output file basename"/>
33 <conditional name="optional" >
34 <param name="file_opt" type="select" label="Optional files" >
35 <option value="none" selected="true">No</option>
36 <option value="fasta">Fasta</option>
37 <option value="fasta_gff">Fasta and GFF</option>
38 </param>
39 <when value="none" />
40 <when value="fasta">
41 <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
42 </when>
43 <when value="fasta_gff">
44 <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
45 <param name="filegff" type="data" format="gff" optional="false" label="GFF file input" help="VCF file must be annotated" />
46 </when>
47 </conditional>
48 </inputs>
49
50 <!-- [REQUIRED] Output files -->
51 <outputs>
52 <data name="fileout" format="txt" label="${fileout_label}.hapmap" />
53 <data name="fileout_seq" format="txt" label="${fileout_label}.flanking.txt">
54 <filter>(optional['file_opt'] != 'none')</filter>
55 </data>
56 <data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas">
57 <filter>(optional['file_opt'] == 'fasta_gff')</filter>
58 </data>
59 </outputs>
60
61 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
62 <stdio>
63 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
64 <exit_code range="1:" level="fatal" />
65 </stdio>
66
67 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
68 <tests>
69 <!-- [HELP] Test files have to be in the ~/test-data directory -->
70 <test>
71 <param name="filein" value="sample.vcf" />
72 <param name="otpional.file_opt" value="none" />
73 <output name="fileout" file="result1.hapmap" />
74 </test>
75 <test>
76 <param name="filein" value="sample.vcf" />
77 <param name="otpional.file_opt" value="fasta" />
78 <param name="filefasta" value="reference.fa" />
79 <output name="fileout" file="result2.hapmap" />
80 <output name="fileout_seq" file="result2.flanking.txt" />
81 <output name="fileout_fa1" file="result2.gene_alignment.fas" />
82 </test>
83 </tests>
84
85 <!-- [OPTIONAL] Help displayed in Galaxy -->
86 <help>
87
88
89 .. class:: infomark
90
91 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
92
93 | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1).
94
95 .. class:: infomark
96
97 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
98
99 .. class:: infomark
100
101 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
102
103 ---------------------------------------------------
104
105 =======================
106 VCF to Hapmap
107 =======================
108
109 -----------
110 Description
111 -----------
112
113 | Convert VCF to Hapmap. Additionnaly it creates flanking sequences of variants if fasta reference is provided.
114 | Furthermore it also creates fasta alignment of genes if GFF annotation is provided
115
116 -----------------
117 Workflow position
118 -----------------
119
120 **Upstream tool**
121
122 =============== ========================== =======
123 Name output file(s) format
124 =============== ========================== =======
125 VCFtools Filter VCF file VCF
126 =============== ========================== =======
127
128
129 **Downstream tool**
130
131 =============== ========================== ===========
132 Name input file(s) format
133 =============== ========================== ===========
134 SNP density Hapmap file tabular
135 =============== ========================== ===========
136
137
138 ----------
139 Input file
140 ----------
141
142 VCF file
143 VCF file with all SNPs
144
145 ----------
146 Parameters
147 ----------
148
149 Output file basename
150 Prefix for the output VCF file
151
152 Optional files
153 To add additional files fasta file and GFF file.
154
155 ------------
156 Output files
157 ------------
158
159 Hapmap file
160 Hapmap converted file
161
162 Additional files
163 If you add fasta and/or GFF file as reference, you obtain 3 more files : One with flanking sequence and a fasta file
164
165 ---------------------------------------------------
166
167 ---------------
168 Working example
169 ---------------
170
171 Input files
172 ===========
173
174 VCF file
175 ---------
176
177 ::
178
179 #fileformat=VCFv4.1
180 #FILTER=&lt;ID=LowQual,Description="Low quality">
181 #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
182 [...]
183 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
184 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
185
186 Fasta file
187 ----------
188
189
190 ::
191
192 >chr1
193 CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTT
194
195 Parameters
196 ==========
197
198 Output name -> input
199
200 Optional files -> Fasta
201
202
203 Output files
204 ============
205
206 input.hapmap
207 ------------
208
209 ::
210
211 rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode CATB1
212 chr1:2209 G/T chr1 2209 + NA NA NA NA NA NA GG TT
213 chr1:2232 A/C chr1 2232 + NA NA NA NA NA NA AA CC
214
215 input.flanking.txt
216 ------------------
217
218 ::
219
220 chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward
221 chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward
222
223 input.gene_alignment.fas
224 ------------------------
225
226 ::
227
228 >chr1_CATB1_1
229 TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT
230
231
232 </help>
233
234 <citations>
235 <!-- [HELP] As DOI or BibTex entry -->
236 <citation type="bibtex">@article{Dereeper03062015,
237 author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel},
238 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
239 year = {2015},
240 doi = {10.1093/nar/gkv351},
241 abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.},
242 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
243 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
244 journal = {Nucleic Acids Research}
245 }
246
247 }</citation>
248
249 </citations>
250
251 </tool>