Mercurial > repos > iuc > gprofiler_orth

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit 4d4576623a85b58137f9e8c5a7747cb2f484c8b6"
author iuc
date Mon, 18 Nov 2019 22:52:39 +0000
parents b10073300e23
children
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b10073300e23 "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"?>
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2 <tool id="gprofiler_orth" name="gProfiler Orth" version="@VERSION@">
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3 <description>translates gene identifiers between organisms</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"></expand>
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8 <expand macro="version_command" />
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9 <command detect_errors="aggressive">Rscript $script_file</command>
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10 <configfiles>
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11 <configfile name="script_file"><![CDATA[
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12
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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13 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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14 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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16 suppressPackageStartupMessages({
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17 library("gprofiler2")
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18 })
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20 set_user_agent(paste(get_user_agent(), "galaxy"))
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21 sessionInfo()
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23 #if $tool_settings.base_url
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24 set_base_url('${tool_settings.base_url}')
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25 #end if
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26
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27 #if $max
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28 mthreshold <- $max
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29 #else
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30 mthreshold = Inf
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31 #end if
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32
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33 query <- scan('${input.file_name}', character(), quote = "")
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34
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35 response <- gorth( query
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36 , source_organism = '${source.organism}'
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37 , target_organism = '${target.organism}'
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38 , numeric_ns = '${numeric_ns}'
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39 , mthreshold = mthreshold
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40 , filter_na = ${filter_na}
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41 )
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42
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43 output <- response
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44 output.colnames = colnames(output)
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45 write.table(output, file='${output}', quote=FALSE, sep='\t', row.names = FALSE, col.names = output.colnames)
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46
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47 ]]></configfile>
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48 </configfiles>
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49 <inputs>
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50 <expand macro="input" />
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51 <expand macro="organism" name="source" label="Source organism" />
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52 <expand macro="organism" name="target" label="Target organism" hsapiens_selected="false" mmusculus_selected="true" />
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53 <param name="numeric_ns" type="text" value="" optional="true" label="Numeric IDs treated as" help="The prefix for fully numeric IDs. Check the “Resources” section below for the complete list of supported namespaces (including numeric). E.g., ENTREZGENE_ACC, WIKIGENE_ACC." />
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54 <param name="max" type="integer" value="" optional="true" label="Maximum number of ortholog names per gene to show" help="Shows all by default." />
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55 <expand macro="filter_na" />
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56 <expand macro="tool_settings"></expand>
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57 </inputs>
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58 <outputs>
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59 <data label="${tool.name} on ${on_string}" name="output" format="tabular" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input" ftype="txt" value="example_query.txt" />
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64 <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
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65 <output name="output" ftype="tabular" file="example_orth_results.txt" sort="true" />
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66 </test>
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67 <test>
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68 <param name="input" ftype="txt" value="example_query_2.txt" />
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69 <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
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70 <conditional name="source">
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71 <param name="organism" value="mmusculus" />
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72 </conditional>
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73 <conditional name="target">
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74 <param name="organism" value="hsapiens" />
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75 </conditional>
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76 <param name="numeric_ns" value="WIKIGENE_ACC" />
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77 <param name="max" value="1" />
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78 <param name="filter_na" value="T" />
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79 <output name="output" ftype="tabular" file="example_orth_results_2.txt" sort="true" />
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80 </test>
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81 </tests>
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82
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83 <help><![CDATA[
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84
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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85 **What it does**
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86 This tool wraps gprofiler2 R package which performs a request to g:Profiler g:Orth tool through its API.
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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87 g:Profiler g:Orth retrieves the genes of the target organism that are similar in sequence to the source organism
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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88 genes in the input.
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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89
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90 -----
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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91
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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92 @REFERENCES@
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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93
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94 ]]></help>
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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95 <expand macro="citations"></expand>
b10073300e23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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96 </tool>