Mercurial > repos > dereeper > sniplay
annotate Rooting/rooting.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 | 15b23cdde685 |
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1 <tool id="sniplay_rooting" name="Rooting" version="2.0.0"> |
| 9 | 2 |
| 3 <!-- [REQUIRED] Tool description displayed after the tool name --> | |
| 4 <description> Midpoint rooting of newick tree </description> | |
| 5 | |
| 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> | |
| 7 <requirements> | |
| 8 <requirement type="binary">perl</requirement> | |
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9 <requirement type="package" version="1.6.924">perl-bioperl</requirement> |
| 9 | 10 </requirements> |
| 11 | |
| 12 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
| 13 <stdio> | |
| 14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 15 <exit_code range="1:" level="fatal" /> | |
| 16 </stdio> | |
| 17 | |
| 18 | |
| 19 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | |
| 20 <version_command> | |
| 21 <!-- | |
| 22 tool_binary -v | |
| 23 --> | |
| 24 </version_command> | |
| 25 | |
| 26 <!-- [REQUIRED] The command to execute --> | |
| 27 <command interpreter="perl"> | |
| 28 Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log | |
| 29 </command> | |
| 30 | |
| 31 <!-- [REQUIRED] Input files and tool parameters --> | |
| 32 <inputs> | |
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33 <param name="filein" type="data" format="nhx" optional="false" label="Newick tree input" /> |
| 9 | 34 <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> |
| 35 </inputs> | |
| 36 | |
| 37 <!-- [REQUIRED] Output files --> | |
| 38 <outputs> | |
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39 <data name="fileout_log" format="txt" label="${fileout_label}.log" /> |
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40 <data name="fileout" format="nhx" label="${fileout_label}" /> |
| 9 | 41 </outputs> |
| 42 | |
| 43 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
| 44 <tests> | |
| 45 <!-- [HELP] Test files have to be in the ~/test-data directory --> | |
| 46 <test> | |
| 47 <param name="filein" value="rooting-newick" /> | |
| 48 <output name="fileout" file="rooting-out_tree" /> | |
| 49 </test> | |
| 50 </tests> | |
| 51 | |
| 52 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
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53 <help><![CDATA[ |
| 9 | 54 |
| 55 .. class:: infomark | |
| 56 | |
| 57 **Authors** Jean-François Dufayard, CIRAD, South Green platform | |
| 58 | |
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59 | **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). |
| 9 | 60 |
| 61 .. class:: infomark | |
| 62 | |
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63 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 9 | 64 |
| 65 .. class:: infomark | |
| 66 | |
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67 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 68 |
| 69 --------------------------------------------------- | |
| 70 | |
| 71 ======= | |
| 72 Rooting | |
| 73 ======= | |
| 74 | |
| 75 ----------- | |
| 76 Description | |
| 77 ----------- | |
| 78 | |
| 79 Compute a midpoint newick rooted tree. | |
| 80 | |
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81 ------------ |
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82 Dependencies |
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83 ------------ |
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84 Bioperl |
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85 perl-bioperl_ 1.6.924, Conda version |
| 9 | 86 |
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87 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl |
| 9 | 88 |
| 89 ---------- | |
| 90 Input file | |
| 91 ---------- | |
| 92 | |
| 93 Newick file | |
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94 Input tree file |
| 9 | 95 |
| 96 ---------- | |
| 97 Parameters | |
| 98 ---------- | |
| 99 | |
| 100 Output name | |
| 101 Output base name for the ouput files | |
| 102 | |
| 103 | |
| 104 ------------ | |
| 105 Output files | |
| 106 ------------ | |
| 107 | |
| 108 Output_name | |
| 109 Resulting tree rooted in newick format | |
| 110 | |
| 111 Output_name.log | |
| 112 Log file | |
| 113 | |
| 114 ------------ | |
| 115 Dependencies | |
| 116 ------------ | |
| 117 Rooting | |
| 118 CIRAD tool. Contact jean-francois.dufayard@cirad.fr | |
| 119 | |
| 120 --------------------------------------------------- | |
| 121 | |
| 122 --------------- | |
| 123 Working example | |
| 124 --------------- | |
| 125 | |
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126 Input file |
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127 ========== |
| 9 | 128 |
| 129 Newick file | |
| 130 ----------- | |
| 131 | |
| 132 :: | |
| 133 | |
| 134 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ... | |
| 135 | |
| 136 | |
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137 Parameter |
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138 ========= |
| 9 | 139 |
| 140 Output name -> out tree | |
| 141 | |
| 142 | |
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143 Output file |
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144 =========== |
| 9 | 145 |
| 146 out tree | |
| 147 -------- | |
| 148 | |
| 149 :: | |
| 150 | |
| 151 (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662... | |
| 152 | |
| 153 | |
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154 ]]></help> |
| 9 | 155 <citations> |
| 156 <!-- [HELP] As DOI or BibTex entry --> | |
| 157 <citation type="bibtex">@article{Dereeper03062015, | |
| 158 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}, | |
| 159 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 160 year = {2015}, | |
| 161 doi = {10.1093/nar/gkv351}, | |
| 162 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.}, | |
| 163 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 164 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 165 journal = {Nucleic Acids Research} | |
| 166 } | |
| 167 | |
| 168 </citation> | |
| 169 | |
| 170 </citations> | |
| 171 | |
| 172 </tool> |