Mercurial > repos > dereeper > sniplay
annotate PedToFasta/pedToFasta.xml @ 10:c6640c49fd01 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
| author | dereeper |
|---|---|
| date | Mon, 16 Apr 2018 09:00:24 -0400 |
| parents | 98c37a5d67f4 |
| children |
| rev | line source |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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1 <tool id="sniplay_pedToFasta" name="Ped2Fasta" version="2.0.0"> |
| 9 | 2 |
| 3 <!-- [REQUIRED] Tool description displayed after the tool name --> | |
| 4 <description> Convert PED file to Fasta File </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="perl"> | |
| 26 Ped2Fasta.pl --in $filein --out $fileout | |
| 27 </command> | |
| 28 | |
| 29 <!-- [REQUIRED] Input files and tool parameters --> | |
| 30 <inputs> | |
| 31 <param name="filein" type="data" format="txt" optional="false" label="PED input" /> | |
| 32 <param name="fileout_label" type="text" value="filtered" optional="false" label="Output file name"/> | |
| 33 </inputs> | |
| 34 | |
| 35 <!-- [REQUIRED] Output files --> | |
| 36 <outputs> | |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
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37 <data name="fileout" format="fasta" label="${fileout_label}.fa" /> |
| 9 | 38 </outputs> |
| 39 | |
| 40 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 41 <tests> | |
| 42 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
| 43 <test> | |
| 44 <param name="filein" value="ped2fasta-sample.ped" /> | |
| 45 <output name="fileout" file="ped2fasta-result.fa" /> | |
| 46 </test> | |
| 47 </tests> | |
| 48 | |
| 49 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
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50 <help><![CDATA[ |
| 9 | 51 |
| 52 .. class:: infomark | |
| 53 | |
| 54 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform | |
| 55 | |
| 56 | **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). | |
| 57 | |
| 58 .. class:: infomark | |
| 59 | |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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60 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 9 | 61 |
| 62 .. class:: infomark | |
| 63 | |
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64 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 65 |
| 66 --------------------------------------------------- | |
| 67 | |
| 68 ========= | |
| 69 Ped2Fasta | |
| 70 ========= | |
| 71 | |
| 72 ----------- | |
| 73 Description | |
| 74 ----------- | |
| 75 | |
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76 | Convert PED file to Fasta File |
| 9 | 77 |
| 78 ---------- | |
| 79 Input file | |
| 80 ---------- | |
| 81 | |
| 82 PED file | |
| 83 PED file usually from VCF tools | |
| 84 | |
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85 --------- |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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86 Parameter |
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87 --------- |
| 9 | 88 |
| 89 Output file name | |
| 90 Prefix for the output fasta file | |
| 91 | |
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92 ----------- |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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93 Output file |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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94 ----------- |
| 9 | 95 |
| 96 Fasta file | |
| 97 PED file conversion | |
| 98 | |
| 99 --------------------------------------------------- | |
| 100 | |
| 101 --------------- | |
| 102 Working example | |
| 103 --------------- | |
| 104 | |
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105 Input file |
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106 ========== |
| 9 | 107 |
| 108 PED file | |
| 109 --------- | |
| 110 | |
| 111 :: | |
| 112 | |
| 113 CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A | |
| 114 | |
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115 Parameter |
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116 ========= |
| 9 | 117 |
| 118 Output name -> pedFile | |
| 119 | |
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120 Output file |
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121 =========== |
| 9 | 122 |
| 123 pedFile.fa | |
| 124 ---------- | |
| 125 | |
| 126 :: | |
| 127 | |
| 128 YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY | |
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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
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129 ]]></help> |
| 9 | 130 |
| 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> |