[2] | 1 | <tool id="hgv_david" name="DAVID" version="1.0.0"> |
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| 2 | <description>functional annotation for a list of genes</description> |
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| 3 | |
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| 4 | <command interpreter="perl"> |
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| 5 | linkToDavid.pl $input $numerical_column $type $out_file1 |
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| 6 | </command> |
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| 7 | |
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| 8 | <inputs> |
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| 9 | <param name="input" type="data" format="tabular" label="Dataset" /> |
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| 10 | <param name="numerical_column" type="data_column" data_ref="input" label="Column with identifiers" /> |
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| 11 | <param name="type" label="Identifier type" type="select"> |
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| 12 | <option value="AFFYMETRIX_3PRIME_IVT_ID">AFFYMETRIX_3PRIME_IVT_ID</option> |
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| 13 | <option value="AFFYMETRIX_EXON_GENE_ID">AFFYMETRIX_EXON_GENE_ID</option> |
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| 14 | <option value="AFFYMETRIX_SNP_ID">AFFYMETRIX_SNP_ID</option> |
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| 15 | <option value="AGILENT_CHIP_ID">AGILENT_CHIP_ID</option> |
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| 16 | <option value="AGILENT_ID">AGILENT_ID</option> |
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| 17 | <option value="AGILENT_OLIGO_ID">AGILENT_OLIGO_ID</option> |
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| 18 | <option value="ENSEMBL_GENE_ID">ENSEMBL_GENE_ID</option> |
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| 19 | <option value="ENSEMBL_TRANSCRIPT_ID">ENSEMBL_TRANSCRIPT_ID</option> |
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| 20 | <option value="ENTREZ_GENE_ID">ENTREZ_GENE_ID</option> |
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| 21 | <option value="FLYBASE_GENE_ID">FLYBASE_GENE_ID</option> |
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| 22 | <option value="FLYBASE_TRANSCRIPT_ID">FLYBASE_TRANSCRIPT_ID</option> |
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| 23 | <option value="GENBANK_ACCESSION">GENBANK_ACCESSION</option> |
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| 24 | <option value="GENPEPT_ACCESSION">GENPEPT_ACCESSION</option> |
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| 25 | <option value="GENOMIC_GI_ACCESSION">GENOMIC_GI_ACCESSION</option> |
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| 26 | <option value="PROTEIN_GI_ACCESSION">PROTEIN_GI_ACCESSION</option> |
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| 27 | <option value="ILLUMINA_ID">ILLUMINA_ID</option> |
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| 28 | <option value="IPI_ID">IPI_ID</option> |
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| 29 | <option value="MGI_ID">MGI_ID</option> |
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| 30 | <option value="GENE_SYMBOL" selected="true">GENE_SYMBOL</option> |
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| 31 | <option value="PFAM_ID">PFAM_ID</option> |
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| 32 | <option value="PIR_ACCESSION">PIR_ACCESSION</option> |
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| 33 | <option value="PIR_ID">PIR_ID</option> |
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| 34 | <option value="PIR_NREF_ID">PIR_NREF_ID</option> |
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| 35 | <option value="REFSEQ_GENOMIC">REFSEQ_GENOMIC</option> |
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| 36 | <option value="REFSEQ_MRNA">REFSEQ_MRNA</option> |
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| 37 | <option value="REFSEQ_PROTEIN">REFSEQ_PROTEIN</option> |
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| 38 | <option value="REFSEQ_RNA">REFSEQ_RNA</option> |
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| 39 | <option value="RGD_ID">RGD_ID</option> |
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| 40 | <option value="SGD_ID">SGD_ID</option> |
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| 41 | <option value="TAIR_ID">TAIR_ID</option> |
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| 42 | <option value="UCSC_GENE_ID">UCSC_GENE_ID</option> |
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| 43 | <option value="UNIGENE">UNIGENE</option> |
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| 44 | <option value="UNIPROT_ACCESSION">UNIPROT_ACCESSION</option> |
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| 45 | <option value="UNIPROT_ID">UNIPROT_ID</option> |
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| 46 | <option value="UNIREF100_ID">UNIREF100_ID</option> |
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| 47 | <option value="WORMBASE_GENE_ID">WORMBASE_GENE_ID</option> |
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| 48 | <option value="WORMPEP_ID">WORMPEP_ID</option> |
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| 49 | <option value="ZFIN_ID">ZFIN_ID</option> |
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| 50 | </param> |
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| 51 | </inputs> |
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| 52 | |
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| 53 | <outputs> |
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| 54 | <data format="html" name="out_file1" /> |
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| 55 | </outputs> |
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| 56 | |
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| 57 | <tests> |
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| 58 | <test> |
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| 59 | <param name="input" ftype="tabular" value="linkToDavid.tabular" /> |
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| 60 | <param name="numerical_column" value="1" /> |
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| 61 | <param name="type" value="ENTREZ_GENE_ID" /> |
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| 62 | <output name="out_file1" file="linkToDavid_1.out" /> |
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| 63 | </test> |
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| 64 | </tests> |
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| 65 | |
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| 66 | <help> |
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| 67 | .. class:: infomark |
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| 68 | |
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| 69 | The list is limited to 400 IDs. |
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| 70 | |
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| 71 | ----- |
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| 72 | |
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| 73 | **Dataset formats** |
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| 74 | |
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| 75 | The input dataset is in tabular_ format. The output dataset is html_ with |
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| 76 | a link to the DAVID website as described below. |
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| 77 | (`Dataset missing?`_) |
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| 78 | |
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| 79 | .. _tabular: ./static/formatHelp.html#tab |
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| 80 | .. _html: ./static/formatHelp.html#html |
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| 81 | .. _Dataset missing?: ./static/formatHelp.html |
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| 82 | |
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| 83 | ----- |
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| 84 | |
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| 85 | **What it does** |
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| 86 | |
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| 87 | This tool creates a link to the Database for Annotation, |
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| 88 | Visualization, and Integrated Discovery (DAVID) website at NIH, |
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| 89 | sending a list of IDs from the selected column of a tabular |
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| 90 | Galaxy dataset. To follow the created link, click on the |
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| 91 | eye icon once the Galaxy tool has finished running. |
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| 92 | |
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| 93 | DAVID provides a comprehensive set of functional annotation tools |
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| 94 | to help investigators discover biological meaning behind large |
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| 95 | lists of genes. |
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| 96 | |
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| 97 | ----- |
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| 98 | |
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| 99 | **References** |
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| 100 | |
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| 101 | Huang DW, Sherman BT, Lempicki RA. (2009) Systematic and integrative analysis |
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| 102 | of large gene lists using DAVID bioinformatics resources. |
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| 103 | Nat Protoc. 4(1):44-57. |
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| 104 | |
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| 105 | Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. (2003) |
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| 106 | DAVID: database for annotation, visualization, and integrated discovery. |
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| 107 | Genome Biol. 4(5):P3. Epub 2003 Apr 3. |
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| 108 | |
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| 109 | </help> |
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| 110 | </tool> |
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