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1 <tool id="hgv_linkToGProfile" name="g:Profiler" version="1.0.0">
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2 <description>tools for functional profiling of gene lists</description>
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3
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4 <command interpreter="perl">
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5 linkToGProfile.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" numerical="True" label="Column with identifiers" />
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11 <param name="type" label="Identifier type" type="select">
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12 <option value="ENTREZGENE_ACC" selected="true">Entrez Gene Acc</option>
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13 <option value="MIM_MORBID">OMIM Morbid Map</option>
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14 <option value="MIM_GENE">OMIM Gene ID</option>
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15 <option value="AFFY_HUGENE_1_0_ST_V1">AFFY_HUGENE_1_0_ST_V1</option>
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16 <option value="HGNC_AUTOMATIC_GENE_ACC">HGNC_AUTOMATIC_GENE_ACC</option>
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17 <option value="HGNC_MB001_ACC">HGNC_MB001_ACC</option>
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18 <option value="HGNC_ACC">HGNC_ACC</option>
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19 <option value="WIKIGENE_ACC">WIKIGENE_ACC</option>
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20 <option value="DBASS5_ACC">DBASS5_ACC</option>
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21 <option value="ILLUMINA_HUMANWG_6_V1">ILLUMINA_HUMANWG_6_V1</option>
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22 <option value="AFFY_HUEX_1_0_ST_V2">AFFY_HUEX_1_0_ST_V2</option>
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23 <option value="DBASS3_ACC">DBASS3_ACC</option>
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24 </param>
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25 </inputs>
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26
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27 <outputs>
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28 <data format="html" name="out_file1" />
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29 </outputs>
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30
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31 <tests>
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32 <test>
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33 <param name="input" ftype="tabular" value="linkToGProfile.tabular" />
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34 <param name="numerical_column" value="2" />
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35 <param name="type" value="ENTREZGENE_ACC" />
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36 <output name="out_file1" file="linkToGProfile_1.out" />
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37 </test>
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38 </tests>
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39
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40 <help>
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41 **Dataset formats**
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42
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43 The input dataset is tabular_ with a column of identifiers.
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44 The output dataset is html_ with a link to g:Profiler.
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45 (`Dataset missing?`_)
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46
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47 .. _tabular: ./static/formatHelp.html#tab
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48 .. _html: ./static/formatHelp.html#html
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49 .. _Dataset missing?: ./static/formatHelp.html
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50
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51 -----
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52
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53 **What it does**
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54
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55 This tool creates a link to the g:GOSt tool (Gene Group Functional
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56 Profiling), which is part of the g:Profiler site at the University
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57 of Tartu in Estonia. g:GOSt retrieves the most significant Gene
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58 Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs
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59 for a user-specified group of genes, proteins, or microarray probes.
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60 g:GOSt also allows analysis of ranked or ordered lists of genes,
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61 visual browsing of GO graph structure, interactive visualization of
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62 retrieved results, and many other features. Multiple testing
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63 corrections are applied to extract only statistically important
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64 results.
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65
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66 The g:GOSt form is pre-filled with gene, protein, or microarray probe
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67 IDs from the selected column of a tabular Galaxy dataset. To follow
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68 the created link, click on the eye icon when the Galaxy tool has
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69 finished running. Once at the g:Profiler site, scroll down to see
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70 the g:GOSt results. You can also adjust the options in the g:GOSt
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71 form to your liking, or use the row of links between the form and
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72 the results to run other g:Profiler tools using the same list of IDs.
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73
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74 -----
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75
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76 **Reference**
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77
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78 Reimand J, Kull M, Peterson H, Hansen J, Vilo J. (2007) g:Profiler -- a web-based
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79 toolset for functional profiling of gene lists from large-scale experiments.
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80 Nucleic Acids Res. 35(Web Server issue):W193-200. Epub 2007 May 3.
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81
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82 </help>
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83 </tool>
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