1
+ − 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=<ID=LowQual,Description="Low quality">
+ − 181 #FORMAT=<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>