root/galaxy-central/tools/human_genome_variation/linkToDavid.xml

リビジョン 2, 4.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
69The list is limited to 400 IDs.
70
71-----
72
73**Dataset formats**
74
75The input dataset is in tabular_ format.  The output dataset is html_ with
76a 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
87This tool creates a link to the Database for Annotation,
88Visualization, and Integrated Discovery (DAVID) website at NIH,
89sending a list of IDs from the selected column of a tabular
90Galaxy dataset.  To follow the created link, click on the
91eye icon once the Galaxy tool has finished running.
92
93DAVID provides a comprehensive set of functional annotation tools
94to help investigators discover biological meaning behind large
95lists of genes.
96
97-----
98
99**References**
100
101Huang DW, Sherman BT, Lempicki RA. (2009) Systematic and integrative analysis
102of large gene lists using DAVID bioinformatics resources.
103Nat Protoc. 4(1):44-57.
104
105Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. (2003)
106DAVID: database for annotation, visualization, and integrated discovery.
107Genome Biol. 4(5):P3. Epub 2003 Apr 3.
108
109  </help>
110</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。