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comparison tools/human_genome_variation/linkToGProfile.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_linkToGProfile" name="g:Profiler" version="1.0.0">
2 <description>tools for functional profiling of gene lists</description>
3
4 <command interpreter="perl">
5 linkToGProfile.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" numerical="True" label="Column with identifiers" />
11 <param name="type" label="Identifier type" type="select">
12 <option value="ENTREZGENE_ACC" selected="true">Entrez Gene Acc</option>
13 <option value="MIM_MORBID">OMIM Morbid Map</option>
14 <option value="MIM_GENE">OMIM Gene ID</option>
15 <option value="AFFY_HUGENE_1_0_ST_V1">AFFY_HUGENE_1_0_ST_V1</option>
16 <option value="HGNC_AUTOMATIC_GENE_ACC">HGNC_AUTOMATIC_GENE_ACC</option>
17 <option value="HGNC_MB001_ACC">HGNC_MB001_ACC</option>
18 <option value="HGNC_ACC">HGNC_ACC</option>
19 <option value="WIKIGENE_ACC">WIKIGENE_ACC</option>
20 <option value="DBASS5_ACC">DBASS5_ACC</option>
21 <option value="ILLUMINA_HUMANWG_6_V1">ILLUMINA_HUMANWG_6_V1</option>
22 <option value="AFFY_HUEX_1_0_ST_V2">AFFY_HUEX_1_0_ST_V2</option>
23 <option value="DBASS3_ACC">DBASS3_ACC</option>
24 </param>
25 </inputs>
26
27 <outputs>
28 <data format="html" name="out_file1" />
29 </outputs>
30
31 <tests>
32 <test>
33 <param name="input" ftype="tabular" value="linkToGProfile.tabular" />
34 <param name="numerical_column" value="2" />
35 <param name="type" value="ENTREZGENE_ACC" />
36 <output name="out_file1" file="linkToGProfile_1.out" />
37 </test>
38 </tests>
39
40 <help>
41 **Dataset formats**
42
43 The input dataset is tabular_ with a column of identifiers.
44 The output dataset is html_ with a link to g:Profiler.
45 (`Dataset missing?`_)
46
47 .. _tabular: ./static/formatHelp.html#tab
48 .. _html: ./static/formatHelp.html#html
49 .. _Dataset missing?: ./static/formatHelp.html
50
51 -----
52
53 **What it does**
54
55 This tool creates a link to the g:GOSt tool (Gene Group Functional
56 Profiling), which is part of the g:Profiler site at the University
57 of Tartu in Estonia. g:GOSt retrieves the most significant Gene
58 Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs
59 for a user-specified group of genes, proteins, or microarray probes.
60 g:GOSt also allows analysis of ranked or ordered lists of genes,
61 visual browsing of GO graph structure, interactive visualization of
62 retrieved results, and many other features. Multiple testing
63 corrections are applied to extract only statistically important
64 results.
65
66 The g:GOSt form is pre-filled with gene, protein, or microarray probe
67 IDs from the selected column of a tabular Galaxy dataset. To follow
68 the created link, click on the eye icon when the Galaxy tool has
69 finished running. Once at the g:Profiler site, scroll down to see
70 the g:GOSt results. You can also adjust the options in the g:GOSt
71 form to your liking, or use the row of links between the form and
72 the results to run other g:Profiler tools using the same list of IDs.
73
74 -----
75
76 **Reference**
77
78 Reimand J, Kull M, Peterson H, Hansen J, Vilo J. (2007) g:Profiler -- a web-based
79 toolset for functional profiling of gene lists from large-scale experiments.
80 Nucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3.
81
82 </help>
83 </tool>