annotate clusterProfiler_bitr.xml @ 9:762c61c71874 draft default tip

Uploaded
author kpbioteam
date Fri, 10 May 2019 06:46:19 -0400
parents 8556126fd733
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
1 <tool id="clusterprofiler_bitr" name="Cluster Profiler Bitr" version="0.1.0">
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
2 <description>converting ID types</description>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
3 <requirements>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
4 <requirement type="package" version="3.10.1">bioconductor-clusterprofiler</requirement>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
5 <requirement type="package" version="3.7.0">bioconductor-org.hs.eg.db</requirement>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
6 </requirements>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
8 Rscript '$clusterprofiler_bitr_script'
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
9 ]]></command>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
10 <configfiles>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
11 <configfile name="clusterprofiler_bitr_script"><![CDATA[
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
12 require("clusterProfiler", quietly = TRUE)
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
13 require("org.Hs.eg.db", quietly = TRUE)
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
14
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
15 gene <- c(read.table('$genelist'))
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
16 gene.df = bitr(gene\$V1, fromType='$fromType', toType='$toType', OrgDb="org.Hs.eg.db")
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
17
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
18 write.table(gene.df,file = '$translation',row.names = FALSE)
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
19
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
20 ]]>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
21 </configfile>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
22 </configfiles>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
23 <inputs>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
24 <param type="data" name="genelist" format="txt" />
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
25 <param name="fromType" type="select" label="Input Type Gene ID" help="User should provides fromType geneID (translator input type)">
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
26 <option value="SYMBOL">SYMBOL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
27 <option value="ENTREZID">ENTREZID</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
28 <option value="ENSEMBL">ENSEMBL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
29 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
30 <option value="EVIDENCE">EVIDENCE</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
31 <option value="GOALL">GOALL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
32
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
33 <option value="ONTOLOGY">ONTOLOGY</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
34 <option value="PMID">PMID</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
35
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
36 <option value="PFAM">PFAM</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
37
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
38 <option value="OMIM">OMIM</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
39
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
40 <option value="GO">GO</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
41
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
42 <option value="UNIPROT">UNIPROT</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
43 <option value="REFSEQ">REFSEQ</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
44 <option value="PATH">PATH</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
45
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
46 <option value="MAP">MAP</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
47
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
48 <option value="GENENAME">GENENAME</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
49 <option value="ENZYME">ENZYME</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
50 <option value="ALIAS">ALIAS</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
51
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
52 <option value="UNIGENE">UNIGENE</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
53 <option value="PROSITE">PROSITE</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
54 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
55 <option value="IPI">IPI</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
56
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
57 <option value="EVIDENCEALL">EVIDENCEALL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
58 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
59 <option value="ACCNUM">ACCNUM</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
60 </param>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
61
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
62 <param name="toType" type="select" label="Output Type Gene ID" help="User should provides toType geneID (translator output type)">
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
63 <option value="SYMBOL">SYMBOL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
64 <option value="ENTREZID">ENTREZID</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
65 <option value="ENSEMBL">ENSEMBL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
66 <option value="ENSEMBLPROT">ENSEMBLPROT</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
67 <option value="EVIDENCE">EVIDENCE</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
68 <option value="GOALL">GOALL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
69
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
70 <option value="ONTOLOGY">ONTOLOGY</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
71 <option value="PMID">PMID</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
72
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
73 <option value="PFAM">PFAM</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
74
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
75 <option value="OMIM">OMIM</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
76
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
77 <option value="GO">GO</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
78
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
79 <option value="UNIPROT">UNIPROT</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
80 <option value="REFSEQ">REFSEQ</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
81 <option value="PATH">PATH</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
82
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
83 <option value="MAP">MAP</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
84
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
85 <option value="GENENAME">GENENAME</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
86 <option value="ENZYME">ENZYME</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
87 <option value="ALIAS">ALIAS</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
88
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
89 <option value="UNIGENE">UNIGENE</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
90 <option value="PROSITE">PROSITE</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
91 <option value="ONTOLOGYALL">ONTOLOGYALL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
92 <option value="IPI">IPI</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
93
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
94 <option value="EVIDENCEALL">EVIDENCEALL</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
95 <option value="ENSEMBLTRANS">ENSEMBLTRANS</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
96 <option value="ACCNUM">ACCNUM</option>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
97 </param>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
98 </inputs>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
99 <outputs>
9
762c61c71874 Uploaded
kpbioteam
parents: 8
diff changeset
100 <data name="translation" format="txt" label="Table of Translated Gene ID's" />
8
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
101 </outputs>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
102 <tests>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
103 <test>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
104 <param name="genelist" value="gene.txt"/>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
105 <param name="fromType" value="SYMBOL"/>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
106 <param name="toType" value="ENTREZID"/>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
107 <output name="translation" file="genedf.txt"/>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
108 </test>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
109 </tests>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
110 <help><![CDATA[
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
111 This tool is a Biological Id TRanslator
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
112 ]]></help>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
113 <citations>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
114 <citation type="doi">10.1089/omi.2011.0118</citation>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
115 </citations>
8556126fd733 Uploaded
kpbioteam
parents:
diff changeset
116 </tool>