Mercurial > repos > dereeper > sniplay
annotate hapmap2mlmm/HapmapToMLMMFiles.xml @ 14:d15869b3731a draft
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| author | dereeper |
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| date | Tue, 08 Jan 2019 08:46:57 -0500 |
| parents | c6640c49fd01 |
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1 <tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="2.0.0"> |
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2 <description>Converts a hapmap file into MLMM input files</description> |
| 9 | 3 <!-- [STRONGLY RECOMMANDED] Exit code rules --> |
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4 <requirements> |
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5 <requirement type="package" version="4.1.3">gawk</requirement> |
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6 </requirements> |
| 9 | 7 <stdio> |
| 8 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 9 <exit_code range="1:" level="fatal" /> | |
| 10 </stdio> | |
| 11 <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="txt" name="snp_info" label="SNP Info file"/> | |
| 18 <data format="txt" name="genot" label="Genotyping file for MLMM"/> | |
| 19 </outputs> | |
| 20 | |
| 21 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 22 <tests> | |
| 23 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
| 24 <!-- [HELP] Multiple tests can be defined with different parameters --> | |
| 25 | |
| 26 <test> | |
| 27 <param name="input" value="hapmap2mlmm-hapmap" /> | |
| 28 <output name="snp_info" file="hapmap2mlmm-result_snp.hapmap" /> | |
| 29 <output name="genot" file="hapmap2mlmm-result_genot" /> | |
| 30 </test> | |
| 31 </tests> | |
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32 <help><![CDATA[ |
| 9 | 33 |
| 34 .. class:: infomark | |
| 35 | |
| 36 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform | |
| 37 | |
| 38 | **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). | |
| 39 | |
| 40 .. class:: infomark | |
| 41 | |
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42 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) |
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43 |
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44 .. class:: infomark |
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45 |
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46 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 47 |
| 48 --------------------------------------------------- | |
| 49 | |
| 50 ================= | |
| 51 HapmapToMLMMFiles | |
| 52 ================= | |
| 53 | |
| 54 ----------- | |
| 55 Description | |
| 56 ----------- | |
| 57 | |
| 58 | HapmapToMLMMFiles converts a hapmap file into input files compatible with the MLMM software. | |
| 59 | |
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60 ------------ |
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61 Dependencies |
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62 ------------ |
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63 GAWK |
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64 gawk_ 4.1.3, Conda version |
| 9 | 65 |
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66 .. _gawk: https://anaconda.org/bioconda/gawk |
| 9 | 67 |
| 68 ---------- | |
| 69 Input file | |
| 70 ---------- | |
| 71 | |
| 72 Hapmap file | |
| 73 Allelic file in Hapmap format | |
| 74 | |
| 75 | |
| 76 | |
| 77 ------------ | |
| 78 Output files | |
| 79 ------------ | |
| 80 | |
| 81 SNP Info file | |
| 82 | |
| 83 Genotyping file for MLMM | |
| 84 | |
| 85 | |
| 86 | |
| 87 --------------------------------------------------- | |
| 88 | |
| 89 --------------- | |
| 90 Working example | |
| 91 --------------- | |
| 92 | |
| 93 Input files | |
| 94 =========== | |
| 95 | |
| 96 Hapmap file | |
| 97 ----------- | |
| 98 | |
| 99 :: | |
| 100 | |
| 101 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 | |
| 102 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA | |
| 103 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA | |
| 104 | |
| 105 | |
| 106 Output files | |
| 107 ============ | |
| 108 | |
| 109 SNP Info file | |
| 110 ------------- | |
| 111 | |
| 112 :: | |
| 113 | |
| 114 SNP Chr Pos | |
| 115 SNP1 1 3102 | |
| 116 SNP2 1 4648 | |
| 117 SNP3 1 7601 | |
| 118 | |
| 119 | |
| 120 Genotyping file for MLMM | |
| 121 ------------------------ | |
| 122 | |
| 123 :: | |
| 124 | |
| 125 Ind_id SNP1 SNP2 SNP3 SNP4 SNP5 SNP6 SNP7 SNP8 SNP9 SNP10 SNP11 SNP12 SNP13 SNP14 | |
| 126 Ind1 0 0 0 0 0 0 2 0 2 0 0 0 2 0 | |
| 127 Ind2 0 0 0 0 0 2 2 0 0 0 0 0 0 0 | |
| 128 | |
| 129 | |
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130 ]]></help> |
| 9 | 131 <citations> |
| 132 <!-- [HELP] As DOI or BibTex entry --> | |
| 133 <citation type="bibtex">@article{Dereeper03062015, | |
| 134 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}, | |
| 135 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 136 year = {2015}, | |
| 137 doi = {10.1093/nar/gkv351}, | |
| 138 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.}, | |
| 139 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 140 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 141 journal = {Nucleic Acids Research} | |
| 142 } | |
| 143 | |
| 144 </citation> | |
| 145 | |
| 146 </citations> | |
| 147 </tool> |