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comparison VCF2Hapmap/vcf2FastaAndHapmap.xml @ 9:98c37a5d67f4 draft

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author dereeper
date Wed, 07 Feb 2018 22:08:47 -0500
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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 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
12 <stdio>
13 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
14 <exit_code range="1:" level="fatal" />
15 </stdio>
16
17 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
18 <version_command>
19 <!--
20 tool_binary -v
21 -->
22 </version_command>
23
24 <!-- [REQUIRED] The command to execute -->
25 <command interpreter="bash">
26 vcf2FastaAndHapmap.sh $filein $fileout $optional.file_opt
27 #if str( $optional.file_opt ) != "none":
28 $fileout_seq $fileout_fa1 $filefasta
29 #if str( $optional.file_opt ) == "fasta_gff":
30 $filegff
31 #end if
32 #end if
33 </command>
34
35 <!-- [REQUIRED] Input files and tool parameters -->
36 <inputs>
37 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
38 <param name="fileout_label" type="text" value="input" optional="false" label="Output file basename"/>
39 <conditional name="optional" >
40 <param name="file_opt" type="select" label="Optional files" >
41 <option value="none" selected="true">No</option>
42 <option value="fasta">Fasta</option>
43 <option value="fasta_gff">Fasta and GFF</option>
44 </param>
45 <when value="none" />
46 <when value="fasta">
47 <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
48 </when>
49 <when value="fasta_gff">
50 <param name="filefasta" type="data" format="fasta" optional="false" label="Fasta file input" />
51 <param name="filegff" type="data" format="gff" optional="false" label="GFF file input" help="VCF file must be annotated" />
52 </when>
53 </conditional>
54 </inputs>
55
56 <!-- [REQUIRED] Output files -->
57 <outputs>
58 <data name="fileout" format="txt" label="${fileout_label}.hapmap" />
59 <data name="fileout_seq" format="txt" label="${fileout_label}.flanking.txt">
60 <filter>(optional['file_opt'] != 'none')</filter>
61 </data>
62 <data name="fileout_fa1" format="fasta" label="${fileout_label}.gene_alignment.fas">
63 <filter>(optional['file_opt'] == 'fasta_gff')</filter>
64 </data>
65 </outputs>
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="vcf2fastaAndHapmap-sample.vcf" />
72 <param name="file_opt" value="none" />
73 <output name="fileout" file="vcf2fastaAndHapmap-result1.hapmap" />
74 </test>
75 <test>
76 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
77 <param name="file_opt" value="fasta" />
78 <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
79 <output name="fileout" file="vcf2fastaAndHapmap-result2.hapmap" />
80 <output name="fileout_seq" file="vcf2fastaAndHapmap-result2.flanking.txt" />
81 </test>
82 <test>
83 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" />
84 <param name="file_opt" value="fasta_gff" />
85 <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" />
86 <param name="filegff" value="vcf2fastaAndHapmap-reference.gff" />
87 <output name="fileout" file="vcf2fastaAndHapmap-result3.hapmap" />
88 <output name="fileout_seq" file="vcf2fastaAndHapmap-result3.flanking.txt" />
89 <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" />
90 </test>
91 </tests>
92
93 <!-- [OPTIONAL] Help displayed in Galaxy -->
94 <help>
95
96
97 .. class:: infomark
98
99 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
100
101 | **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).
102
103 .. class:: infomark
104
105 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
106
107 .. class:: infomark
108
109 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
110
111 ---------------------------------------------------
112
113 =======================
114 VCF to Hapmap
115 =======================
116
117 -----------
118 Description
119 -----------
120
121 | Convert VCF to Hapmap. Additionnaly it creates flanking sequences of variants if fasta reference is provided.
122 | Furthermore it also creates fasta alignment of genes if GFF annotation is provided
123
124 -----------------
125 Workflow position
126 -----------------
127
128 **Upstream tool**
129
130 =============== ========================== =======
131 Name output file(s) format
132 =============== ========================== =======
133 VCFtools Filter VCF file VCF
134 =============== ========================== =======
135
136
137 **Downstream tool**
138
139 =============== ========================== ===========
140 Name input file(s) format
141 =============== ========================== ===========
142 SNP density Hapmap file tabular
143 =============== ========================== ===========
144
145
146 ----------
147 Input file
148 ----------
149
150 VCF file
151 VCF file with all SNPs
152
153 ----------
154 Parameters
155 ----------
156
157 Output file basename
158 Prefix for the output VCF file
159
160 Optional files
161 To add additional files fasta file and GFF file.
162
163 ------------
164 Output files
165 ------------
166
167 Hapmap file
168 Hapmap converted file
169
170 Additional files
171 If you add fasta and/or GFF file as reference, you obtain 3 more files : One with flanking sequence and a fasta file
172
173 ---------------------------------------------------
174
175 ---------------
176 Working example
177 ---------------
178
179 Input files
180 ===========
181
182 VCF file
183 ---------
184
185 ::
186
187 #fileformat=VCFv4.1
188 #FILTER=&lt;ID=LowQual,Description="Low quality">
189 #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
190 [...]
191 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1
192 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
193
194 Fasta file
195 ----------
196
197
198 ::
199
200 >chr1
201 CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTT
202
203 Parameters
204 ==========
205
206 Output name -> input
207
208 Optional files -> Fasta
209
210
211 Output files
212 ============
213
214 input.hapmap
215 ------------
216
217 ::
218
219 rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode CATB1
220 chr1:2209 G/T chr1 2209 + NA NA NA NA NA NA GG TT
221 chr1:2232 A/C chr1 2232 + NA NA NA NA NA NA AA CC
222
223 input.flanking.txt
224 ------------------
225
226 ::
227
228 chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward
229 chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward
230
231 input.gene_alignment.fas
232 ------------------------
233
234 ::
235
236 >chr1_CATB1_1
237 TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT
238
239
240 </help>
241
242 <citations>
243 <!-- [HELP] As DOI or BibTex entry -->
244 <citation type="bibtex">@article{Dereeper03062015,
245 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},
246 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
247 year = {2015},
248 doi = {10.1093/nar/gkv351},
249 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.},
250 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
251 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
252 journal = {Nucleic Acids Research}
253 }
254
255 }</citation>
256
257 </citations>
258
259 </tool>