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

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<tool id="hgv_david" name="DAVID" version="1.0.0">
  <description>functional annotation for a list of genes</description>

  <command interpreter="perl">
    linkToDavid.pl $input $numerical_column $type $out_file1
  </command>

  <inputs>
    <param name="input" type="data" format="tabular" label="Dataset" />
    <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" />
    <param name="type" label="Identifier type" type="select">
      <option value="AFFYMETRIX_3PRIME_IVT_ID">AFFYMETRIX_3PRIME_IVT_ID</option>
      <option value="AFFYMETRIX_EXON_GENE_ID">AFFYMETRIX_EXON_GENE_ID</option>
      <option value="AFFYMETRIX_SNP_ID">AFFYMETRIX_SNP_ID</option>
      <option value="AGILENT_CHIP_ID">AGILENT_CHIP_ID</option>
      <option value="AGILENT_ID">AGILENT_ID</option>
      <option value="AGILENT_OLIGO_ID">AGILENT_OLIGO_ID</option>
      <option value="ENSEMBL_GENE_ID">ENSEMBL_GENE_ID</option>
      <option value="ENSEMBL_TRANSCRIPT_ID">ENSEMBL_TRANSCRIPT_ID</option>
      <option value="ENTREZ_GENE_ID">ENTREZ_GENE_ID</option>
      <option value="FLYBASE_GENE_ID">FLYBASE_GENE_ID</option>
      <option value="FLYBASE_TRANSCRIPT_ID">FLYBASE_TRANSCRIPT_ID</option>
      <option value="GENBANK_ACCESSION">GENBANK_ACCESSION</option>
      <option value="GENPEPT_ACCESSION">GENPEPT_ACCESSION</option>
      <option value="GENOMIC_GI_ACCESSION">GENOMIC_GI_ACCESSION</option>
      <option value="PROTEIN_GI_ACCESSION">PROTEIN_GI_ACCESSION</option>
      <option value="ILLUMINA_ID">ILLUMINA_ID</option>
      <option value="IPI_ID">IPI_ID</option>
      <option value="MGI_ID">MGI_ID</option>
      <option value="GENE_SYMBOL" selected="true">GENE_SYMBOL</option>
      <option value="PFAM_ID">PFAM_ID</option>
      <option value="PIR_ACCESSION">PIR_ACCESSION</option>
      <option value="PIR_ID">PIR_ID</option>
      <option value="PIR_NREF_ID">PIR_NREF_ID</option>
      <option value="REFSEQ_GENOMIC">REFSEQ_GENOMIC</option>
      <option value="REFSEQ_MRNA">REFSEQ_MRNA</option>
      <option value="REFSEQ_PROTEIN">REFSEQ_PROTEIN</option>
      <option value="REFSEQ_RNA">REFSEQ_RNA</option>
      <option value="RGD_ID">RGD_ID</option>
      <option value="SGD_ID">SGD_ID</option>
      <option value="TAIR_ID">TAIR_ID</option>
      <option value="UCSC_GENE_ID">UCSC_GENE_ID</option>
      <option value="UNIGENE">UNIGENE</option>
      <option value="UNIPROT_ACCESSION">UNIPROT_ACCESSION</option>
      <option value="UNIPROT_ID">UNIPROT_ID</option>
      <option value="UNIREF100_ID">UNIREF100_ID</option>
      <option value="WORMBASE_GENE_ID">WORMBASE_GENE_ID</option>
      <option value="WORMPEP_ID">WORMPEP_ID</option>
      <option value="ZFIN_ID">ZFIN_ID</option>
    </param>
  </inputs>

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

  <tests>
    <test>
      <param name="input" ftype="tabular" value="linkToDavid.tabular" />
      <param name="numerical_column" value="1" />
      <param name="type" value="ENTREZ_GENE_ID" />
      <output name="out_file1" file="linkToDavid_1.out" />
    </test>
  </tests>

  <help>
 .. class:: infomark

The list is limited to 400 IDs.

-----

**Dataset formats**

The input dataset is in tabular_ format.  The output dataset is html_ with
a link to the DAVID website as described below.
(`Dataset missing?`_)

.. _tabular: ./static/formatHelp.html#tab
.. _html: ./static/formatHelp.html#html
.. _Dataset missing?: ./static/formatHelp.html

-----

**What it does**

This tool creates a link to the Database for Annotation,
Visualization, and Integrated Discovery (DAVID) website at NIH,
sending a list of IDs from the selected column of a tabular
Galaxy dataset.  To follow the created link, click on the
eye icon once the Galaxy tool has finished running.

DAVID provides a comprehensive set of functional annotation tools
to help investigators discover biological meaning behind large
lists of genes.

-----

**References**

Huang DW, Sherman BT, Lempicki RA. (2009) Systematic and integrative analysis
of large gene lists using DAVID bioinformatics resources.
Nat Protoc. 4(1):44-57.

Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. (2003)
DAVID: database for annotation, visualization, and integrated discovery.
Genome Biol. 4(5):P3. Epub 2003 Apr 3.

  </help>
</tool>