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1 <tool id="data_manager_fetch_gff" name="Create entries in gff data table" version="0.0.1" tool_type="manage_data">
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2 <description>fetching</description>
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3 <command><![CDATA[
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4 python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}"
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5 --type $file_type
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6 #if str( $dbkey_source.dbkey_source_selector ) == 'existing':
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7 --dbkey_description ${ dbkey_source.dbkey.get_display_text() }
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8 #else
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9 --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }"
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10 #end if
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11
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12 ]]></command>
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13 <inputs>
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14 <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file">
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15 <option value="representative">Representative GFF</option>
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16 <option value="full">GFF with complete features</option>
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17 </param>
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18
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19 <conditional name="dbkey_source">
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20 <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one.">
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21 <option value="existing" selected="True">Existing</option>
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22 <option value="new">New</option>
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23 </param>
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24 <when value="existing">
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25 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
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26 </when>
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27 <when value="new">
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28 <param type="text" name="dbkey" value="" label="dbkey" optional="False" />
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29 <param type="text" name="dbkey_name" value="" label="Display name for dbkey" />
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30 </when>
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31 </conditional>
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32 <param type="text" name="sequence_name" value="" label="Name of sequence" />
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33 <param type="text" name="sequence_id" value="" label="ID for sequence" />
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34 <conditional name="reference_source">
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35 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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36 <option value="url">URL</option>
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37 <option value="history">History</option>
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38 <option value="directory">Directory on Server</option>
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39 </param>
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40 <when value="url">
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41 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
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42 </when>
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43 <when value="history">
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44 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
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45 </when>
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46 <when value="directory">
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47 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
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48 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
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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 <!-- TODO: need some way to test that new entry was added to data table -->
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57 <test>
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58 <param name="dbkey" value="anoGam1"/>
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59 <param name="sequence_name" value=""/>
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60 <param name="sequence_desc" value=""/>
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61 <param name="sequence_id" value=""/>
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62 <param name="reference_source_selector" value="history"/>
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63 <param name="input_fasta" value="phiX174.fasta"/>
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64 <param name="sort_selector" value="as_is"/>
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65 <output name="out_file" file="phiX174.data_manager_json"/>
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66 </test>
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67 </tests>
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68 <help>
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69 **What it does**
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70
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71 Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table.
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72
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73 ------
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74
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75
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76
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77 .. class:: infomark
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78
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79 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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80
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81 </help>
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82 </tool>
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