Mercurial > repos > dereeper > sniplay
annotate check_gwas_inputs/CheckGWASInputs.xml @ 15:31c23d943c29 draft default tip
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| author | dereeper |
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| date | Tue, 08 Jan 2019 08:47:56 -0500 |
| parents | c6640c49fd01 |
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1 <tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="2.0.0"> |
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2 <description>Checks concordance between input files for GWAS analysis</description> |
| 9 | 3 |
| 4 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> | |
| 5 <requirements> | |
| 6 <requirement type="binary">perl</requirement> | |
| 7 </requirements> | |
| 8 | |
| 9 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
| 10 <stdio> | |
| 11 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 12 <exit_code range="1:" level="fatal" /> | |
| 13 </stdio> | |
| 14 | |
| 15 <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param format="txt" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> | |
| 19 <param format="txt" name="trait" type="data" label="Trait file" help="Phenotypic file"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="txt" name="out_hapmap" label="Hapmap output"/> | |
| 23 <data format="txt" name="out_trait" label="Trait output"/> | |
| 24 <data format="txt" name="stats" label="Logfile and statistics"/> | |
| 25 </outputs> | |
| 26 | |
| 27 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 28 <tests> | |
| 29 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
| 30 <!-- [HELP] Multiple tests can be defined with different parameters --> | |
| 31 <test> | |
| 32 <param name="hapmap" value="gwas-hapmap" /> | |
| 33 <param name="trait" value="gwas-trait" /> | |
| 34 <output name="out_hapmap" file="gwas-result.hapmap" /> | |
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35 <output name="out_trait" file="gwas-result.trait" compare="sim_size" delta="0"/> |
| 9 | 36 <output name="stats" file="gwas-result.stats" /> |
| 37 </test> | |
| 38 </tests> | |
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39 <help><![CDATA[ |
| 9 | 40 |
| 41 .. class:: infomark | |
| 42 | |
| 43 **Authors** South Green | |
| 44 | |
| 45 | **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). | |
| 46 | |
| 47 .. class:: infomark | |
| 48 | |
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49 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) |
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50 |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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51 .. class:: infomark |
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52 |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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53 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 54 |
| 55 --------------------------------------------------- | |
| 56 | |
| 57 =============== | |
| 58 CheckGWASInputs | |
| 59 =============== | |
| 60 | |
| 61 ----------- | |
| 62 Description | |
| 63 ----------- | |
| 64 | |
| 65 | CheckGWASInputs checks concordance between input files for GWAS analysis. | |
| 66 | |
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67 ----------- |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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68 Input files |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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69 ----------- |
| 9 | 70 |
| 71 Hapmap file | |
| 72 Allelic file in Hapmap format | |
| 73 | |
| 74 Trait file | |
| 75 Phenotypic file | |
| 76 | |
| 77 ------------ | |
| 78 Output files | |
| 79 ------------ | |
| 80 | |
| 81 Hapmap output | |
| 82 | |
| 83 Trait output | |
| 84 | |
| 85 Logfile and statistics | |
| 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 Trait file | |
| 106 ---------- | |
| 107 | |
| 108 :: | |
| 109 | |
| 110 <Trait> Test | |
| 111 Ind1 -2.9985936006411 | |
| 112 Ind2 -2.68669426456267 | |
| 113 | |
| 114 Output files | |
| 115 ============ | |
| 116 | |
| 117 Hapmap output | |
| 118 ------------- | |
| 119 | |
| 120 :: | |
| 121 | |
| 122 rs# alleles chrom pos strand assembly# center protLSID assayLSID panel QCcode Ind1 Ind2 Ind3 Ind4 | |
| 123 SNP1 A/T 1 3102 + assembly NA NA NA speciesname NA AA AA AA AA AA | |
| 124 SNP2 A/T 1 4648 + assembly NA NA NA speciesname NA AA AA AA AA TT | |
| 125 | |
| 126 | |
| 127 Trait output | |
| 128 ------------ | |
| 129 | |
| 130 :: | |
| 131 | |
| 132 <Trait> Test | |
| 133 Ind429 -26.2142525264157 | |
| 134 Ind373 12.0306115988504 | |
| 135 Ind81 1.98118654229534 | |
| 136 | |
| 137 Logfile and statistics | |
| 138 ---------------------- | |
| 139 | |
| 140 :: | |
| 141 | |
| 142 | |
| 143 ============================================== | |
| 144 Individuals | |
| 145 ============================================== | |
| 146 Individuals in hapmap file: 500 | |
| 147 Individuals in trait file: 500 | |
| 148 Individuals found in both files: 500 | |
| 149 ============================================== | |
| 150 Markers | |
| 151 ============================================== | |
| 152 Discarded markers: | |
| 153 Monomorphic: 0 | |
| 154 Not biallelic: 0 | |
| 155 Modified markers: | |
| 156 Difference in variation: 0 | |
| 157 | |
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158 ]]></help> |
| 9 | 159 <citations> |
| 160 <!-- [HELP] As DOI or BibTex entry --> | |
| 161 <citation type="bibtex">@article{Dereeper03062015, | |
| 162 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}, | |
| 163 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 164 year = {2015}, | |
| 165 doi = {10.1093/nar/gkv351}, | |
| 166 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.}, | |
| 167 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 168 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 169 journal = {Nucleic Acids Research} | |
| 170 } | |
| 171 | |
| 172 </citation> | |
| 173 | |
| 174 </citations> | |
| 175 </tool> |