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1 <tool id="clusterprofiler_bitr" name="Cluster Profiler Bitr" version="0.1.0">
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2 <description>converting ID types</description>
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3 <requirements>
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4 <requirement type="package" version="3.10.1">bioconductor-clusterprofiler</requirement>
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5 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$clusterprofiler_bitr_script'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="clusterprofiler_bitr_script"><![CDATA[
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12 require("clusterProfiler", quietly = TRUE)
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13 require("org.Hs.eg.db", quietly = TRUE)
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14
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15 gene <- c(read.table('$genelist'))
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16 gene.df = bitr(gene\$V1, fromType='$fromType', toType='$toType', OrgDb="org.Hs.eg.db")
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17
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18 write.table(gene.df,file = '$translation',row.names = FALSE)
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19
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20 ]]>
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21 </configfile>
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22 </configfiles>
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23 <inputs>
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24 <param type="data" name="genelist" format="txt" />
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25 <param name="fromType" type="select" label="Input Type Gene ID" help="User should provides fromType geneID (translator input type)">
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26 <option value="SYMBOL">SYMBOL</option>
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27 <option value="ENTREZID">ENTREZID</option>
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28 <option value="ENSEMBL">ENSEMBL</option>
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29 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
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30 <option value="EVIDENCE">EVIDENCE</option>
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31 <option value="GOALL">GOALL</option>
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32
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33 <option value="ONTOLOGY">ONTOLOGY</option>
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34 <option value="PMID">PMID</option>
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35
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36 <option value="PFAM">PFAM</option>
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37
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38 <option value="OMIM">OMIM</option>
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39
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40 <option value="GO">GO</option>
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41
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42 <option value="UNIPROT">UNIPROT</option>
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43 <option value="REFSEQ">REFSEQ</option>
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44 <option value="PATH">PATH</option>
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45
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46 <option value="MAP">MAP</option>
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47
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48 <option value="GENENAME">GENENAME</option>
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49 <option value="ENZYME">ENZYME</option>
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50 <option value="ALIAS">ALIAS</option>
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51
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52 <option value="UNIGENE">UNIGENE</option>
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53 <option value="PROSITE">PROSITE</option>
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54 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
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55 <option value="IPI">IPI</option>
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56
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57 <option value="EVIDENCEALL">EVIDENCEALL</option>
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58 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
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59 <option value="ACCNUM">ACCNUM</option>
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60 </param>
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61
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62 <param name="toType" type="select" label="Output Type Gene ID" help="User should provides toType geneID (translator output type)">
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63 <option value="SYMBOL">SYMBOL</option>
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64 <option value="ENTREZID">ENTREZID</option>
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65 <option value="ENSEMBL">ENSEMBL</option>
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66 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
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67 <option value="EVIDENCE">EVIDENCE</option>
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68 <option value="GOALL">GOALL</option>
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69
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70 <option value="ONTOLOGY">ONTOLOGY</option>
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71 <option value="PMID">PMID</option>
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72
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73 <option value="PFAM">PFAM</option>
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74
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75 <option value="OMIM">OMIM</option>
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76
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77 <option value="GO">GO</option>
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78
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79 <option value="UNIPROT">UNIPROT</option>
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80 <option value="REFSEQ">REFSEQ</option>
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81 <option value="PATH">PATH</option>
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82
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83 <option value="MAP">MAP</option>
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84
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85 <option value="GENENAME">GENENAME</option>
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86 <option value="ENZYME">ENZYME</option>
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87 <option value="ALIAS">ALIAS</option>
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88
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89 <option value="UNIGENE">UNIGENE</option>
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90 <option value="PROSITE">PROSITE</option>
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91 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
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92 <option value="IPI">IPI</option>
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93
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94 <option value="EVIDENCEALL">EVIDENCEALL</option>
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95 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
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96 <option value="ACCNUM">ACCNUM</option>
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97 </param>
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98 </inputs>
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99 <outputs>
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9
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100 <data name="translation" format="txt" label="Table of Translated Gene ID's" />
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8
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101 </outputs>
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102 <tests>
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103 <test>
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104 <param name="genelist" value="gene.txt"/>
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105 <param name="fromType" value="SYMBOL"/>
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106 <param name="toType" value="ENTREZID"/>
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107 <output name="translation" file="genedf.txt"/>
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108 </test>
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109 </tests>
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110 <help><![CDATA[
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111 This tool is a Biological Id TRanslator
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112 ]]></help>
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113 <citations>
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114 <citation type="doi">10.1089/omi.2011.0118</citation>
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115 </citations>
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116 </tool>
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