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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 <description>Fetch and install annotation databases for CEAS</description>
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3 <command interpreter="python">data_manager_ceas_fetch_annotations.py
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4 #if str( $reference_source.reference_source_selector ) == "ceas_web"
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5 --download=$reference_source.annotation_url
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6 #end if
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7 "${out_file}"
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8 "${description}"</command>
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9 <inputs>
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10 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
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11 <param type="text" name="description" value="" label="Description of annotation" />
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12 <conditional name="reference_source">
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13 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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14 <option value="ceas_web" selected="True">CEAS website</option>
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15 <!-- Not implemented for now
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16 <option value="history">History</option>
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17 -->
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18 <option value="directory">Directory on Server</option>
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19 </param>
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20 <when value="ceas_web">
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21 <param type="select" name="annotation_url">
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22 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option>
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23 <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz">hg19</option>
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24 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm8.refGene.gz">mm8</option>
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25 <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
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26 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm2.refGene.gz">dm2</option>
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27 <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option>
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28 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce4.refGene.gz">ce4</option>
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29 <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
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30 </param>
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31 </when>
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32 <!-- Not implemented for now
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33 <when value="history">
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34 <param name="input_annotation" type="data" format="fasta" label="Annotation File" multiple="False" optional="False" />
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35 </when>
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36 -->
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37 <when value="directory">
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38 <param type="text" name="annotation_filename" value="" 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 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data name="out_file" format="data_manager_json"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="dbkey" value="anoGam1"/>
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49 <param name="sequence_name" value=""/>
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50 <param name="sequence_desc" value=""/>
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51 <param name="sequence_id" value=""/>
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52 <param name="reference_source_selector" value="history"/>
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53 <param name="input_fasta" value="phiX174.fasta"/>
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54 <param name="sort_selector" value="as_is"/>
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55 <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/>
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56 </test>
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57 </tests>
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58 <help>
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59 **What it does**
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60
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61 Fetches an annotation database from the CEAS website, Galaxy history, or a server directory
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62 and populates the "ceas_annotations" data table.
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63
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64 ------
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65
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66
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67
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68 .. class:: infomark
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69
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70 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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71
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72 </help>
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73 </tool>
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