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comparison tools/human_genome_variation/linkToDavid.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="hgv_david" name="DAVID" version="1.0.0">
2 <description>functional annotation for a list of genes</description>
3
4 <command interpreter="perl">
5 linkToDavid.pl $input $numerical_column $type $out_file1
6 </command>
7
8 <inputs>
9 <param name="input" type="data" format="tabular" label="Dataset" />
10 <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" />
11 <param name="type" label="Identifier type" type="select">
12 <option value="AFFYMETRIX_3PRIME_IVT_ID">AFFYMETRIX_3PRIME_IVT_ID</option>
13 <option value="AFFYMETRIX_EXON_GENE_ID">AFFYMETRIX_EXON_GENE_ID</option>
14 <option value="AFFYMETRIX_SNP_ID">AFFYMETRIX_SNP_ID</option>
15 <option value="AGILENT_CHIP_ID">AGILENT_CHIP_ID</option>
16 <option value="AGILENT_ID">AGILENT_ID</option>
17 <option value="AGILENT_OLIGO_ID">AGILENT_OLIGO_ID</option>
18 <option value="ENSEMBL_GENE_ID">ENSEMBL_GENE_ID</option>
19 <option value="ENSEMBL_TRANSCRIPT_ID">ENSEMBL_TRANSCRIPT_ID</option>
20 <option value="ENTREZ_GENE_ID">ENTREZ_GENE_ID</option>
21 <option value="FLYBASE_GENE_ID">FLYBASE_GENE_ID</option>
22 <option value="FLYBASE_TRANSCRIPT_ID">FLYBASE_TRANSCRIPT_ID</option>
23 <option value="GENBANK_ACCESSION">GENBANK_ACCESSION</option>
24 <option value="GENPEPT_ACCESSION">GENPEPT_ACCESSION</option>
25 <option value="GENOMIC_GI_ACCESSION">GENOMIC_GI_ACCESSION</option>
26 <option value="PROTEIN_GI_ACCESSION">PROTEIN_GI_ACCESSION</option>
27 <option value="ILLUMINA_ID">ILLUMINA_ID</option>
28 <option value="IPI_ID">IPI_ID</option>
29 <option value="MGI_ID">MGI_ID</option>
30 <option value="GENE_SYMBOL" selected="true">GENE_SYMBOL</option>
31 <option value="PFAM_ID">PFAM_ID</option>
32 <option value="PIR_ACCESSION">PIR_ACCESSION</option>
33 <option value="PIR_ID">PIR_ID</option>
34 <option value="PIR_NREF_ID">PIR_NREF_ID</option>
35 <option value="REFSEQ_GENOMIC">REFSEQ_GENOMIC</option>
36 <option value="REFSEQ_MRNA">REFSEQ_MRNA</option>
37 <option value="REFSEQ_PROTEIN">REFSEQ_PROTEIN</option>
38 <option value="REFSEQ_RNA">REFSEQ_RNA</option>
39 <option value="RGD_ID">RGD_ID</option>
40 <option value="SGD_ID">SGD_ID</option>
41 <option value="TAIR_ID">TAIR_ID</option>
42 <option value="UCSC_GENE_ID">UCSC_GENE_ID</option>
43 <option value="UNIGENE">UNIGENE</option>
44 <option value="UNIPROT_ACCESSION">UNIPROT_ACCESSION</option>
45 <option value="UNIPROT_ID">UNIPROT_ID</option>
46 <option value="UNIREF100_ID">UNIREF100_ID</option>
47 <option value="WORMBASE_GENE_ID">WORMBASE_GENE_ID</option>
48 <option value="WORMPEP_ID">WORMPEP_ID</option>
49 <option value="ZFIN_ID">ZFIN_ID</option>
50 </param>
51 </inputs>
52
53 <outputs>
54 <data format="html" name="out_file1" />
55 </outputs>
56
57 <tests>
58 <test>
59 <param name="input" ftype="tabular" value="linkToDavid.tabular" />
60 <param name="numerical_column" value="1" />
61 <param name="type" value="ENTREZ_GENE_ID" />
62 <output name="out_file1" file="linkToDavid_1.out" />
63 </test>
64 </tests>
65
66 <help>
67 .. class:: infomark
68
69 The list is limited to 400 IDs.
70
71 -----
72
73 **Dataset formats**
74
75 The input dataset is in tabular_ format. The output dataset is html_ with
76 a link to the DAVID website as described below.
77 (`Dataset missing?`_)
78
79 .. _tabular: ./static/formatHelp.html#tab
80 .. _html: ./static/formatHelp.html#html
81 .. _Dataset missing?: ./static/formatHelp.html
82
83 -----
84
85 **What it does**
86
87 This tool creates a link to the Database for Annotation,
88 Visualization, and Integrated Discovery (DAVID) website at NIH,
89 sending a list of IDs from the selected column of a tabular
90 Galaxy dataset. To follow the created link, click on the
91 eye icon once the Galaxy tool has finished running.
92
93 DAVID provides a comprehensive set of functional annotation tools
94 to help investigators discover biological meaning behind large
95 lists of genes.
96
97 -----
98
99 **References**
100
101 Huang DW, Sherman BT, Lempicki RA. (2009) Systematic and integrative analysis
102 of large gene lists using DAVID bioinformatics resources.
103 Nat Protoc. 4(1):44-57.
104
105 Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. (2003)
106 DAVID: database for annotation, visualization, and integrated discovery.
107 Genome Biol. 4(5):P3. Epub 2003 Apr 3.
108
109 </help>
110 </tool>