Mercurial > repos > dereeper > sniplay
annotate VCF2Hapmap/vcf2FastaAndHapmap.xml @ 15:31c23d943c29 draft default tip
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| author | dereeper |
|---|---|
| date | Tue, 08 Jan 2019 08:47:56 -0500 |
| parents | c6640c49fd01 |
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| rev | line source |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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1 <tool id="sniplay_vcf2fastaandhapmap" name="VCF to Hapmap" version="2.0.0"> |
| 9 | 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" /> | |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
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diff
changeset
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89 <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" compare="sim_size" delta="0"/> |
| 9 | 90 </test> |
| 91 </tests> | |
| 92 | |
| 93 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
|
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
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94 <help><![CDATA[ |
| 9 | 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 | |
|
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
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changeset
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105 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 9 | 106 |
| 107 .. class:: infomark | |
| 108 | |
|
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
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diff
changeset
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109 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 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 Input file | |
| 126 ---------- | |
| 127 | |
| 128 VCF file | |
| 129 VCF file with all SNPs | |
| 130 | |
| 131 ---------- | |
| 132 Parameters | |
| 133 ---------- | |
| 134 | |
| 135 Output file basename | |
| 136 Prefix for the output VCF file | |
| 137 | |
| 138 Optional files | |
| 139 To add additional files fasta file and GFF file. | |
| 140 | |
| 141 ------------ | |
| 142 Output files | |
| 143 ------------ | |
| 144 | |
| 145 Hapmap file | |
| 146 Hapmap converted file | |
| 147 | |
| 148 Additional files | |
| 149 If you add fasta and/or GFF file as reference, you obtain 3 more files : One with flanking sequence and a fasta file | |
| 150 | |
| 151 --------------------------------------------------- | |
| 152 | |
| 153 --------------- | |
| 154 Working example | |
| 155 --------------- | |
| 156 | |
| 157 Input files | |
| 158 =========== | |
| 159 | |
| 160 VCF file | |
| 161 --------- | |
| 162 | |
| 163 :: | |
| 164 | |
| 165 #fileformat=VCFv4.1 | |
| 166 #FILTER=<ID=LowQual,Description="Low quality"> | |
| 167 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| 168 [...] | |
| 169 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 | |
| 170 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 | |
| 171 | |
| 172 Fasta file | |
| 173 ---------- | |
| 174 | |
| 175 | |
| 176 :: | |
| 177 | |
| 178 >chr1 | |
| 179 CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTT | |
| 180 | |
| 181 Parameters | |
| 182 ========== | |
| 183 | |
| 184 Output name -> input | |
| 185 | |
| 186 Optional files -> Fasta | |
| 187 | |
| 188 | |
| 189 Output files | |
| 190 ============ | |
| 191 | |
| 192 input.hapmap | |
| 193 ------------ | |
| 194 | |
| 195 :: | |
| 196 | |
| 197 rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode CATB1 | |
| 198 chr1:2209 G/T chr1 2209 + NA NA NA NA NA NA GG TT | |
| 199 chr1:2232 A/C chr1 2232 + NA NA NA NA NA NA AA CC | |
| 200 | |
| 201 input.flanking.txt | |
| 202 ------------------ | |
| 203 | |
| 204 :: | |
| 205 | |
| 206 chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward | |
| 207 chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward | |
| 208 | |
| 209 input.gene_alignment.fas | |
| 210 ------------------------ | |
| 211 | |
| 212 :: | |
| 213 | |
| 214 >chr1_CATB1_1 | |
| 215 TCCTCAAACTTTCTTCAGCGCCTATGAATACAGCGTGCTATAGTTACGTGGGGCGTTT | |
| 216 | |
| 217 | |
|
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents:
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diff
changeset
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218 ]]></help> |
| 9 | 219 |
| 220 <citations> | |
| 221 <!-- [HELP] As DOI or BibTex entry --> | |
| 222 <citation type="bibtex">@article{Dereeper03062015, | |
| 223 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}, | |
| 224 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 225 year = {2015}, | |
| 226 doi = {10.1093/nar/gkv351}, | |
| 227 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.}, | |
| 228 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 229 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 230 journal = {Nucleic Acids Research} | |
| 231 } | |
| 232 | |
| 233 }</citation> | |
| 234 | |
| 235 </citations> | |
| 236 | |
| 237 </tool> |