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annotate GetHaplotypesFromPhasedVCF/getHaplotypesFromPhasedVCF.xml @ 12:88748d846a20 draft
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| author | dereeper |
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| date | Tue, 14 Aug 2018 08:21:55 -0400 |
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1 <tool id="getHaplotypesFromPhasedVCF" name="Get Haplotypes From Phased VCF" version="2.0.0"> |
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2 <description>Get Haplotypes From Phased VCF</description> |
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3 |
| 6 | 4 <requirements> |
| 5 <requirement type="binary">perl</requirement> | |
| 6 </requirements> | |
| 7 <stdio> | |
| 8 <exit_code range="1:" /> | |
| 9 </stdio> | |
| 10 <command interpreter="perl"> | |
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11 GetHaplotypesFromPhasedVCF.pl $input $output_label && mv ${output_label}.distinct_haplotypes.txt $output_distinct && mv ${output_label}.haplo.fas $output_haplo && mv ${output_label}.distinct_haplotypes.fa $output_distinct_fasta |
| 6 | 12 </command> |
| 13 <inputs> | |
| 14 <param type="data" name="input" format="vcf" label="Phased VCF" /> | |
| 15 <param type="text" name="output_label" label="Output_label" value='Haplotypes' /> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data name="output_distinct" format="txt" label="${output_label}.distinct_haplotypes.txt"/> | |
| 19 <data name="output_haplo" format="fasta" label="${output_label}.haplo.fas"/> | |
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20 <data name="output_distinct_fasta" format="fasta" label="${output_label}.distinct_haplotypes.fa"/> |
| 6 | 21 </outputs> |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="input" value="getHaplotypesFromPhasedVCF-input.vcf"/> | |
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25 <output name="output_distinct" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.txt" compare="sim_size" delta="0"/> |
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26 <output name="output_haplo" file="getHaplotypesFromPhasedVCF-result.haplo.fas" compare="sim_size" delta="0"/> |
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27 <output name="output_distinct_fasta" file="getHaplotypesFromPhasedVCF-result.distinct_haplotypes.fas" compare="sim_size" delta="0"/> |
| 6 | 28 </test> |
| 29 </tests> | |
| 30 <help><![CDATA[ | |
| 31 | |
| 32 .. class:: infomark | |
| 33 | |
| 34 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform | |
| 35 | |
| 36 | **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). | |
| 37 | |
| 38 .. class:: infomark | |
| 39 | |
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40 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 6 | 41 |
| 42 .. class:: infomark | |
| 43 | |
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44 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 6 | 45 |
| 46 --------------------------------------------------- | |
| 47 | |
| 48 ============================== | |
| 49 Get Haplotypes From Phased VCF | |
| 50 ============================== | |
| 51 | |
| 52 ----------- | |
| 53 Description | |
| 54 ----------- | |
| 55 | |
| 56 | Get Haplotype from phased VCF | |
| 57 | |
| 58 ---------- | |
| 59 Input file | |
| 60 ---------- | |
| 61 | |
| 62 VCF file | |
| 63 Phased VCF file | |
| 64 | |
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65 --------- |
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66 Parameter |
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67 --------- |
| 6 | 68 |
| 69 Output file basename | |
| 70 Prefix for the output VCF file | |
| 71 | |
| 72 ------------ | |
| 73 Output files | |
| 74 ------------ | |
| 75 | |
| 76 | |
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77 Distinct Haplotypes text file |
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78 File describing distincts haplotypes |
| 6 | 79 |
| 80 Fasta file | |
| 81 Fasta file with haplotypes | |
| 82 | |
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83 Distinct Haplotypes fasta file |
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84 Fasta file with distincts haplotypes |
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85 |
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86 |
| 6 | 87 --------------------------------------------------- |
| 88 | |
| 89 --------------- | |
| 90 Working example | |
| 91 --------------- | |
| 92 | |
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93 Input file |
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94 ========== |
| 6 | 95 |
| 96 VCF file | |
| 97 --------- | |
| 98 | |
| 99 :: | |
| 100 | |
| 101 #fileformat=VCFv4.1 | |
| 102 #FILTER=<ID=LowQual,Description="Low quality"> | |
| 103 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| 104 [...] | |
| 105 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA | |
| 106 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0 | |
| 107 | |
| 108 | |
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109 Parameter |
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110 ========= |
| 6 | 111 |
| 112 Output name -> haplotypes | |
| 113 | |
| 114 | |
| 115 Output files | |
| 116 ============ | |
| 117 | |
| 118 haplotypes.distinct_haplotypes.txt | |
| 119 ---------------------------------- | |
| 120 | |
| 121 :: | |
| 122 | |
| 123 ===Chr10=== | |
| 124 haplo1:2:CIRAD403_1,CIRAD403_2, | |
| 125 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT | |
| 126 haplo2:2:MAHAE_1,MAHAE_2, | |
| 127 TAAATCTTGGTGCTGATCTGATATTTAATGCGT | |
| 128 | |
| 129 | |
| 130 haplotypes.haplo.fas | |
| 131 -------------------- | |
| 132 | |
| 133 :: | |
| 134 | |
| 135 >Chr10_AZUCENA_1 | |
| 136 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT | |
| 137 >Chr10_AZUCENA_2 | |
| 138 TAAATCTTGGTGCTGATCTGATATTTAATGCGT | |
| 139 | |
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140 haplotypes.distinct_haplotypes.fas |
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141 ---------------------------------- |
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142 |
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143 :: |
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144 |
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145 >haplo1|2 |
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146 CAATTTATATATACTTGTATATAACCACAACGAGAGAGTTTTACCT |
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147 TTTATAAAAAATAAATAATGTATTACGGCTAATATAGCAATCTTTT |
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148 AAAATAAATCTATATTTAAATGACTATGGAATTACTAATCACAATA |
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149 ACAGGATCTTGTTATTTTTAGCTTGTGTACTTATAATGATCCGATG |
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150 >haplo2|2 |
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151 GCTACTTAAATATCTAGCATTAATCCACAACGAGAGGCTCTTACCT |
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152 TTAAAAAAGGGTCATCGCCTATAGGTTAGATAATCGACACATATAA |
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153 TTATAAGAAATTATATATAATTTTTAATCTAGTTCATTCTTGTGCA |
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154 TCATTATGTTATATAATAATAAACGTAACAAATATTGATACTACTC |
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155 |
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156 |
| 6 | 157 ]]></help> |
| 158 <citations> | |
| 159 <!-- [HELP] As DOI or BibTex entry --> | |
| 160 <citation type="bibtex">@article{Dereeper03062015, | |
| 161 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}, | |
| 162 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 163 year = {2015}, | |
| 164 doi = {10.1093/nar/gkv351}, | |
| 165 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.}, | |
| 166 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 167 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 168 journal = {Nucleic Acids Research} | |
| 169 } | |
| 170 | |
| 171 }</citation> | |
| 172 | |
| 173 </citations> | |
| 174 | |
| 175 </tool> |