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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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