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comparison clusterProfiler_bitr.xml @ 0:74a45de5cca7 draft

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author kpbioteam
date Sun, 28 Apr 2019 03:42:46 -0400
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1 <tool id="clusterprofiler_bitr" name="Cluster Profiler Bitr" version="0.1.0">
2 <description>converting ID types</description>
3 <requirements>
4 <requirement type="package" version="3.6.0">bioconductor-clusterprofiler</requirement>
5 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$clusterprofiler_bitr_script'
9 ]]></command>
10 <configfiles>
11 <configfile name="clusterprofiler_bitr_script"><![CDATA[
12 require("clusterProfiler", quietly = TRUE)
13 require("org.Hs.eg.db", quietly = TRUE)
14
15 gene <- c(read.table('$genelist'))
16 gene.df = bitr(gene\$V1, fromType='$fromType', toType='$toType', OrgDb="org.Hs.eg.db")
17
18 write.table(gene.df,file = '$translation',row.names = FALSE)
19
20 ]]>
21 </configfile>
22 </configfiles>
23 <inputs>
24 <param type="data" name="genelist" format="txt" />
25 <param name="fromType" type="select" label="Input Type Gene ID" help="User should provides fromType geneID (translator input type)">
26 <option value="SYMBOL">SYMBOL</option>
27 <option value="ENTREZID">ENTREZID</option>
28 <option value="ENSEMBL">ENSEMBL</option>
29 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
30 <option value="EVIDENCE">EVIDENCE</option>
31 <option value="GOALL">GOALL</option>
32
33 <option value="ONTOLOGY">ONTOLOGY</option>
34 <option value="PMID">PMID</option>
35
36 <option value="PFAM">PFAM</option>
37
38 <option value="OMIM">OMIM</option>
39
40 <option value="GO">GO</option>
41
42 <option value="UNIPROT">UNIPROT</option>
43 <option value="REFSEQ">REFSEQ</option>
44 <option value="PATH">PATH</option>
45
46 <option value="MAP">MAP</option>
47
48 <option value="GENENAME">GENENAME</option>
49 <option value="ENZYME">ENZYME</option>
50 <option value="ALIAS">ALIAS</option>
51
52 <option value="UNIGENE">UNIGENE</option>
53 <option value="PROSITE">PROSITE</option>
54 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
55 <option value="IPI">IPI</option>
56
57 <option value="EVIDENCEALL">EVIDENCEALL</option>
58 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
59 <option value="ACCNUM">ACCNUM</option>
60 </param>
61
62 <param name="toType" type="select" label="Output Type Gene ID" help="User should provides toType geneID (translator output type)">
63 <option value="SYMBOL">SYMBOL</option>
64 <option value="ENTREZID">ENTREZID</option>
65 <option value="ENSEMBL">ENSEMBL</option>
66 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
67 <option value="EVIDENCE">EVIDENCE</option>
68 <option value="GOALL">GOALL</option>
69
70 <option value="ONTOLOGY">ONTOLOGY</option>
71 <option value="PMID">PMID</option>
72
73 <option value="PFAM">PFAM</option>
74
75 <option value="OMIM">OMIM</option>
76
77 <option value="GO">GO</option>
78
79 <option value="UNIPROT">UNIPROT</option>
80 <option value="REFSEQ">REFSEQ</option>
81 <option value="PATH">PATH</option>
82
83 <option value="MAP">MAP</option>
84
85 <option value="GENENAME">GENENAME</option>
86 <option value="ENZYME">ENZYME</option>
87 <option value="ALIAS">ALIAS</option>
88
89 <option value="UNIGENE">UNIGENE</option>
90 <option value="PROSITE">PROSITE</option>
91 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
92 <option value="IPI">IPI</option>
93
94 <option value="EVIDENCEALL">EVIDENCEALL</option>
95 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
96 <option value="ACCNUM">ACCNUM</option>
97 </param>
98 </inputs>
99 <outputs>
100 <data name="translation" format="txt" />
101 </outputs>
102 <tests>
103 <test>
104 <param name="genelist" value="gene.txt"/>
105 <param name="fromType" value="SYMBOL"/>
106 <param name="toType" value="ENTREZID"/>
107 <output name="translation" file="genedf.txt"/>
108 </test>
109 </tests>
110 <help><![CDATA[
111 This tool is a Biological Id TRanslator
112 ]]></help>
113 <citations>
114 <citation type="doi">10.1089/omi.2011.0118</citation>
115 </citations>
116 </tool>