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/tools/human_genome_variation/linkToGProfile.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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
43The input dataset is tabular_ with a column of identifiers.
44The 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
55This tool creates a link to the g:GOSt tool (Gene Group Functional
56Profiling), which is part of the g:Profiler site at the University
57of Tartu in Estonia.  g:GOSt retrieves the most significant Gene
58Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs
59for a user-specified group of genes, proteins, or microarray probes.
60g:GOSt also allows analysis of ranked or ordered lists of genes,
61visual browsing of GO graph structure, interactive visualization of
62retrieved results, and many other features.  Multiple testing
63corrections are applied to extract only statistically important
64results.
65
66The g:GOSt form is pre-filled with gene, protein, or microarray probe
67IDs from the selected column of a tabular Galaxy dataset.  To follow
68the created link, click on the eye icon when the Galaxy tool has
69finished running.  Once at the g:Profiler site, scroll down to see
70the g:GOSt results.  You can also adjust the options in the g:GOSt
71form to your liking, or use the row of links between the form and
72the results to run other g:Profiler tools using the same list of IDs.
73
74-----
75
76**Reference**
77
78Reimand J, Kull M, Peterson H, Hansen J, Vilo J. (2007) g:Profiler -- a web-based
79toolset for functional profiling of gene lists from large-scale experiments.
80Nucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3.
81
82  </help>
83</tool>