Mercurial > repos > kpbioteam > clusterprofiler_bitr

annotate clusterProfiler_bitr.xml @ 1:90120121398f draft default tip

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planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f-dirty
author kpbioteam
date Mon, 16 Jul 2018 06:25:51 -0400
parents e7a71e686f53
children
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e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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1 <tool id="clusterProfiler_bitr" name="clusterProfiler_bitr" version="0.1.0">
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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2 <description>converting ID types</description>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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3 <requirements>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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4 <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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6 </requirements>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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7 <command detect_errors="exit_code"><![CDATA[
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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8 Rscript ${__tool_directory__}/clusterProfiler_bitr.R "$input1" "$input2" "$input3" "$output1"
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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9 ]]></command>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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10 <inputs>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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11 <param type="data" name="input1" format="txt" />
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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12 <param name="input2" type="select" label="Input Type Gene ID" help="User should provides fromType geneID (translator input type)">
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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13 <option value="SYMBOL">SYMBOL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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14 <option value="ENTREZID">ENTREZID</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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15 <option value="ENSEMBL">ENSEMBL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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16 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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17 <option value="EVIDENCE">EVIDENCE</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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18 <option value="GOALL">GOALL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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20 <option value="ONTOLOGY">ONTOLOGY</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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21 <option value="PMID">PMID</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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23 <option value="PFAM">PFAM</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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25 <option value="OMIM">OMIM</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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27 <option value="GO">GO</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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29 <option value="UNIPROT">UNIPROT</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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30 <option value="REFSEQ">REFSEQ</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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31 <option value="PATH">PATH</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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32
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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33 <option value="MAP">MAP</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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kpbioteam
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35 <option value="GENENAME">GENENAME</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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36 <option value="ENZYME">ENZYME</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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37 <option value="ALIAS">ALIAS</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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38
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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39 <option value="UNIGENE">UNIGENE</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
parents:
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40 <option value="PROSITE">PROSITE</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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41 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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42 <option value="IPI">IPI</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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44 <option value="EVIDENCEALL">EVIDENCEALL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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45 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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46 <option value="ACCNUM">ACCNUM</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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47 </param>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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49 <param name="input3" type="select" label="Output Type Gene ID" help="User should provides toType geneID (translator output type)">
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
parents:
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50 <option value="SYMBOL">SYMBOL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
parents:
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51 <option value="ENTREZID">ENTREZID</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
parents:
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52 <option value="ENSEMBL">ENSEMBL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
parents:
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53 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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54 <option value="EVIDENCE">EVIDENCE</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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55 <option value="GOALL">GOALL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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56
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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57 <option value="ONTOLOGY">ONTOLOGY</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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58 <option value="PMID">PMID</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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59
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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60 <option value="PFAM">PFAM</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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62 <option value="OMIM">OMIM</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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64 <option value="GO">GO</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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65
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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66 <option value="UNIPROT">UNIPROT</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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67 <option value="REFSEQ">REFSEQ</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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68 <option value="PATH">PATH</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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69
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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70 <option value="MAP">MAP</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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72 <option value="GENENAME">GENENAME</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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73 <option value="ENZYME">ENZYME</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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74 <option value="ALIAS">ALIAS</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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75
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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76 <option value="UNIGENE">UNIGENE</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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77 <option value="PROSITE">PROSITE</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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78 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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79 <option value="IPI">IPI</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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80
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81 <option value="EVIDENCEALL">EVIDENCEALL</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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82 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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83 <option value="ACCNUM">ACCNUM</option>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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84 </param>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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85 </inputs>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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86 <outputs>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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87 <data name="output1" format="txt" />
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
kpbioteam
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88 </outputs>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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89 <tests>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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90 <test>
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91 <param name="input1" value="gene.txt"/>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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92 <param name="input2" value="SYMBOL"/>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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93 <param name="input3" value="ENTREZID"/>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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94 <output name="output1" file="genedf.txt"/>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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95 </test>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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96 </tests>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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97 <help><![CDATA[
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98 This tool is a Biological Id TRanslator
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99 ]]></help>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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100 <citations>
e7a71e686f53 planemo upload for repository https://github.com/kpbioteam/clusterProfiler_bitr commit 470dccce41afc79ef1cc7a6722b50d0c258e0f4f
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101 <citation type="doi">10.1089/omi.2011.0118</citation>
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102 </citations>
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103 </tool>