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1 <tool id="data_manager_fetch_tx2gene" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data">
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2 <description>fetching</description>
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3
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3 <requirements>
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4 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
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5 <requirement type="package">r-getopt</requirement>
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6 </requirements>
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7
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8 <command><![CDATA[
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9 python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}"
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10 --type $file_type
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11 --dbkey_description ${ dbkey.get_display_text() }
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12 --base_dir $__tool_directory__
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13
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14 ]]></command>
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15 <inputs>
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16
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17 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
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18 <param type="text" name="sequence_name" value="" label="Name of sequence" />
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19 <param type="text" name="sequence_id" value="" label="ID for sequence" />
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20
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21 <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)">
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22 <option value="gtf">GTF file</option>
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23 <option value="gff3">GFF3 file</option>
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24 <option value="tx2gene">tx2gene</option>
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25 </param>
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26 <conditional name="reference_source">
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27 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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28 <option value="url">URL</option>
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29 <option value="history">History</option>
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30 <option value="directory">Directory on Server</option>
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31 </param>
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32 <when value="url">
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33 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
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34 </when>
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35 <when value="history">
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36 <param name="input_fasta" type="data" label="File from History" multiple="False" optional="False" />
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37 </when>
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38 <when value="directory">
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39 <param type="text" name="filename" value="" label="Full path to File on disk" optional="False" />
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40 <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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41 </when>
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42 </conditional>
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43 </inputs>
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44 <outputs>
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45 <data name="out_file" format="data_manager_json"/>
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46 </outputs>
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47 <tests>
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48 <!-- TODO: need some way to test that new entry was added to data table -->
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49 <test>
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50 <param name="dbkey" value="anoGam1"/>
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51 <param name="sequence_name" value=""/>
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52 <param name="sequence_desc" value=""/>
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53 <param name="sequence_id" value=""/>
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54 <param name="reference_source_selector" value="history"/>
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55 <param name="input_fasta" value="phiX174.fasta"/>
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56 <param name="sort_selector" value="as_is"/>
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57 <output name="out_file" file="phiX174.data_manager_json"/>
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58 </test>
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59 </tests>
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60 <help>
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61 **What it does**
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62
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63 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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64
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65 ------
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66
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67
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68
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69 .. class:: infomark
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70
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71 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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72
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73 </help>
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74 </tool>
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