Mercurial > repos > iuc > gprofiler_convert

annotate macros.xml @ 0:e219aca2f9fc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
author iuc
date Thu, 14 Nov 2019 05:59:47 -0500
parents
children 8ee097f1763d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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1 <?xml version="1.0"?>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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2 <macros>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="@TOOL_VERSION@">r-gprofiler2</requirement>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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6 <requirement type="package" version="2.7.3">pandoc</requirement>
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7 <yield />
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8 </requirements>
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9 </xml>
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10
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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11 <token name="@TOOL_VERSION@">0.1.7</token>
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12 <token name="@VERSION@">@TOOL_VERSION@+galaxy10</token>
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13
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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14 <xml name="version_command">
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15 <version_command>
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16 Rscript -e 'library(gprofiler2); packageVersion("gprofiler2")' | sed 's/\[1\] //' | sed 's/.//;s/.$//'
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17 </version_command>
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18 </xml>
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e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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20 <token name="@REFERENCES@"><![CDATA[
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21
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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22 This tool is part of the `g:Profiler`_ from the `University of Tartu`_.
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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23
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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24 .. _g:Profiler: https://biit.cs.ut.ee/gprofiler/
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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25 .. _University of Tartu: https://ut.ee/en/
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26
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27 **Resources**
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28 * `A complete list of suppоrted organism IDs`_
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29 * `A complete list of supported namespaces`_
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30
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31 .. _A complete list of suppоrted organism IDs: https://biit.cs.ut.ee/gprofiler/page/organism-list
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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32 .. _A complete list of supported namespaces: https://biit.cs.ut.ee/gprofiler/page/namespaces-list
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33
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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34 **gprofiler2 R tool**
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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35 * https://CRAN.R-project.org/package=gprofiler2 — as CRAN package.
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36 * https://anaconda.org/conda-forge/r-gprofiler2 — as conda-forge package.
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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37
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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38 **Contact**
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39 * Contact us at biit.support@ut.ee for further help.
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40
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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41 .. class:: warningmark
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42
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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43 By default the tool makes requests to APIs of the latest g:Profiler instance with the most recent data release.
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44 Please, use ’Tool Settings → Base URL’ to modify it in case you want to make use of older data versions. Also, if the
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45 results should be pinned for reproducibility, we suggest to modify the base url to the last archived data version.
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46
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47 ]]></token>
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48
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49 <xml name="input">
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50 <param name="input" type="data" format="txt" label="Input is whitespace-separated list of genes, proteins, probes, term IDs or chromosomal regions." />
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51 </xml>
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52 <xml name="organism" token_name="organism" token_label="Organism"
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53 token_hsapiens_selected="true" token_mmusculus_selected="false">
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54 <conditional name="@NAME@">
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55 <param name="select_input_type" type="select" label="@LABEL@">
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56 <option value="select">Common organisms</option>
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57 <option value="input">Enter organism ID</option>
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58 </param>
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59 <when value="select">
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60 <param name="organism" type="select" label="Common organisms">
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61 <option value="athaliana">Arabidopsis thaliana</option>
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62 <option value="afumigatusa1163">Aspergillus fumigatus A1163</option>
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63 <option value="btaurus">Bos taurus (Cow)</option>
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64 <option value="celegans">Caenorhabditis elegans</option>
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65 <option value="cfamiliaris">Canis lupus familiaris (Dog)</option>
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66 <option value="drerio">Danio rerio (Zebrafish)</option>
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67 <option value="dmelanogaster">Drosophila melanogaster</option>
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68 <option value="ggallus">Gallus gallus (Chicken)</option>
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69 <option value="hsapiens" selected="@HSAPIENS_SELECTED@">Homo sapiens (Human)</option>
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70 <option value="mmusculus" selected="@MMUSCULUS_SELECTED@">Mus musculus (Mouse)</option>
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71 <option value="osativa">Oryza sativa Japonica Group</option>
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72 <option value="pteres">Pyrenophora teres f. teres 0-1 (Pyrenophora teres)</option>
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73 <option value="rnorvegicus">Rattus norvegicus (Rat)</option>
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74 <option value="scerevisiae">Saccharomyces cerevisiae</option>
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75 <option value="zmays">Zea mays</option>
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76 </param>
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77 </when>
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78 <when value="input">
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79 <param name="organism" type="text" value="hsapiens" label="Enter organism ID" help="Organism IDs are constructed by concatenating the first letter of the generic name and the specific name. E.g., human — Homo sapiens — ’hsapiens’, mouse — Mus musculus — ’mmusculus’, thale cress — Arabidopsis thaliana — ’athaliana’. Check the help section below for the complete list of supported organism IDs." />
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80 </when>
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81 </conditional>
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82 </xml>
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83
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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84 <xml name="filter_na">
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85 <param name="filter_na" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Filter N/A" help="Whether to filter out results without a corresponding target name." />
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86 </xml>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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87
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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88 <xml name="tool_settings">
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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89 <section name="tool_settings" title="Tool settings" expanded="false">
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90 <param type="text" name="base_url" label="Base URL" optional="true" help="Useful for overriding the default URL (http://biit.cs.ut.ee/gprofiler) with the beta (https://biit.cs.ut.ee/gprofiler_beta) or a compatible archived version (available starting from the version e94_eg41_p11, e.g. https://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11)." value="http://biit.cs.ut.ee/gprofiler" />
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91 <yield />
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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92 </section>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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93 </xml>
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94
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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95 <xml name="citations">
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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96 <citations>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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97 <citation type="doi">doi:10.1093/nar/gkz369</citation>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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98 <yield />
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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99 </citations>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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100 </xml>
e219aca2f9fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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101 </macros>