mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
111 lines
4.2 KiB
XML
111 lines
4.2 KiB
XML
<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>
|