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1 <tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
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2 <requirements>
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3 <requirement type="package" version="1.2.5">python_mysqldb</requirement>
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4 <requirement type="package" version="0.7.1">bx_python</requirement>
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5 <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
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6 </requirements>
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7 <description>Fetch and install annotation databases for CEAS</description>
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8 <command interpreter="python">data_manager_ceas_fetch_annotations.py
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9 "${out_file}"
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10 "${description}"</command>
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11 <inputs>
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12 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
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13 <param type="text" name="unique_id" label="Internal identifier"
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14 help="Identifier string to associate with the annotation e.g. 'mm9_generic'" />
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15 <param type="text" name="description" value="" size="50"
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16 label="Description of annotation"
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17 help="Text that will be displayed to the user when selecting which annotation to use" />
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18 <conditional name="reference_source">
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19 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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20 <option value="web" selected="True">CEAS website</option>
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21 <option value="server">File on the server</option>
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22 <option value="from_wig">Generated from wig file</option>
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23 </param>
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24 <when value="web">
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25 <param type="select" name="annotation_url">
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26 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option>
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27 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz">hg19</option>
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28 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm8.refGene.gz">mm8</option>
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29 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
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30 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm2.refGene.gz">dm2</option>
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31 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option>
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32 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce4.refGene.gz">ce4</option>
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33 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
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34 </param>
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35 </when>
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36 <when value="server">
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37 <param type="text" name="annotation_filename" value="" size="50"
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38 label="Full path to CEAS annotation table file on disk" optional="False" />
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39 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
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40 </when>
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41 <when value="from_wig">
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42 <param type="data" format="wig" name="wig_file" value=""
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43 label="Wig file to use for the background genome annotation"
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44 help="Will be used as input to build_genomeBG" />
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45 <param type="select" name="gene_annotation"
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46 label="Gene annotation from UCSC">
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47 <option value="refGene">refGene</option>
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48 </param>
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49 </when>
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50 </conditional>
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51 </inputs>
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52 <outputs>
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53 <data name="out_file" format="data_manager_json"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <!-- No tests defined, yet -->
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58 </test>
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59 </tests>
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60 <help>
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61
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62 .. class:: infomark
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63
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64 **What it does**
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65
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66 Adds a CEAS gene annotation table file to the *ceas_annotations"* data table. The
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67 database file can be downloaded from the CEAS website, imported from a file on the
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68 Galaxy server, or generated from a ``wig`` file in a Galaxy history.
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69
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70 **Notice:** If you leave the identifier or description blank then they will be
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71 generated automatically.
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72
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73 ------
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74
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75 .. class:: infomark
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76
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77 **Fetching, uploading or creating gene annotation table files**
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78
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79 The gene annotation table files are SQLite database files which are on the CEAS website:
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80
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81 - http://liulab.dfci.harvard.edu/CEAS/usermanual.html
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82
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83 The data manager allows you to fetch a pre-built table from the CEAS website; note
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84 that these are based on the ``RefSeq`` annotation and are only available for a subset
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85 of genome builds.
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86
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87 To create an annotation table for a different genome build or a different annotation,
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88 use the *Generated from wig* file option. This runs the CEAS utility ``build_genomeBG``
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89 to make a custom table from a wig file, which represents the genome background (e.g.
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90 a wig file created from the ``control lambda`` bedgraph file output from MACS2).
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91
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92 Alternatively if you already have an existing custom annotation file then this can be
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93 imported from a path on the Galaxy server.
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94 </help>
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95 </tool>
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