galaxy-central / tools / phenotype_association / linkToGProfile.xml

<tool id="hgv_linkToGProfile" name="g:Profiler" version="1.0.0">
  <description>tools for functional profiling of gene lists</description>

  <command interpreter="perl"> $input $type $out_file1 -region=$region -gene=$genes -chr=${input.metadata.chromCol} -start=${input.metadata.startCol} -end=${input.metadata.endCol}

    <param name="input" type="data" format="tabular" label="Dataset" />
    <param name="genes" type="data_column" data_ref="input" label="Column with identifiers" />
    <param name="region" type="select" label="Or use genomic intervals">
      <option value="0" selected="true">No</option>
      <option value="1">Yes</option>
    <param name="type" label="Identifier type if numeric" type="select">
      <option value="ENTREZGENE_ACC" selected="true">Entrez Gene Acc</option>
      <option value="MIM_MORBID">OMIM Morbid Map</option>
      <option value="MIM_GENE">OMIM Gene ID</option>
      <option value="AFFY_HUGENE_1_0_ST_V1">AFFY_HUGENE_1_0_ST_V1</option>
      <option value="HGNC_MB001_ACC">HGNC_MB001_ACC</option>
      <option value="HGNC_ACC">HGNC_ACC</option>
      <option value="WIKIGENE_ACC">WIKIGENE_ACC</option>
      <option value="DBASS5_ACC">DBASS5_ACC</option>
      <option value="ILLUMINA_HUMANWG_6_V1">ILLUMINA_HUMANWG_6_V1</option>
      <option value="AFFY_HUEX_1_0_ST_V2">AFFY_HUEX_1_0_ST_V2</option>
      <option value="DBASS3_ACC">DBASS3_ACC</option>

    <data format="html" name="out_file1" />

      <param name="input" ftype="tabular" value="linkToGProfile.tabular" />
      <param name="genes" value="2" />
      <param name="type" value="ENTREZGENE_ACC" />
      <output name="out_file1" file="linkToGProfile_1.out" />

**Dataset formats**

The input dataset is tabular_ with a column of identifiers.
The output dataset is html_ with a link to g:Profiler.
(`Dataset missing?`_)

.. _tabular: ${static_path}/formatHelp.html#tab
.. _html: ${static_path}/formatHelp.html#html
.. _Dataset missing?: ${static_path}/formatHelp.html


**What it does**

This tool creates a link to the g:GOSt tool (Gene Group Functional
Profiling), which is part of the g:Profiler site at the University
of Tartu in Estonia.  g:GOSt retrieves the most significant Gene
Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs
for a user-specified group of genes, proteins, or microarray probes.
g:GOSt also allows analysis of ranked or ordered lists of genes,
visual browsing of GO graph structure, interactive visualization of
retrieved results, and many other features.  Multiple testing
corrections are applied to extract only statistically important

The g:GOSt form is pre-filled with gene, protein, or microarray probe
IDs from the selected column of a tabular Galaxy dataset.  Or you
can chose to use the genomic coordinates (must be lastest build used by
Ensembl).  The coordinates don't have to be genes they can be for
SNPs, and g:GOst will map to the gene ID.  To follow
the created link, click on the eye icon when the Galaxy tool has
finished running.  Once at the g:Profiler site, scroll down to see
the g:GOSt results.  You can also adjust the options in the g:GOSt
form to your liking, or use the row of links between the form and
the results to run other g:Profiler tools using the same list of IDs.



Reimand J, Kull M, Peterson H, Hansen J, Vilo J. (2007) g:Profiler -- a web-based
toolset for functional profiling of gene lists from large-scale experiments.
Nucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3.