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1 <tool id="build_alfa_indexes" name="ALFA indexes" version="0.0.1" tool_type="manage_data">
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2 <description>build ALFA indexes from automatically downloaded gtf annotation file</description>
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3 <!-- ALFA requires bedtools suite v2.20.0 and above -->
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4 <requirements>
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5 <requirement type="package" version="2.24">bedtools</requirement>
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6 <requirement type="package" version="1.2">samtools</requirement>
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7 <requirement type="package" version="1.4">matplotlib</requirement>
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8 </requirements>
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9
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10 <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" "$__tool_directory__"</command>
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11
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12 <inputs>
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13 <conditional name="reference_source">
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14 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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15 <option value="ensembl" selected="True">Ensembl Genomes Websites</option>
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16 </param>
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17 <when value="ensembl">
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18 <param name="kingdom" type="select" label="Select the ensembl website where to fetch the genome">
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19 <option value="vertebrates" selected="True">Ensembl (Vertebrates)</option>
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20 <option value="bacteria" selected="True">Ensembl Bacteria</option>
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21 <option value="fungi" selected="True">Ensembl Fungi</option>
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22 <option value="metazoa" selected="True">Ensembl Metazoa</option>
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23 <option value="plants" selected="True">Ensembl Plants</option>
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24 <option value="protists" selected="True">Ensembl Protists</option>
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25 </param>
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26 <param name="species_name" type="text" value="Homo sapiens" label="Complete Species_Name" optional="False">
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27 <validator type="empty_field" message="Please, enter a species name."/>
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28 </param>
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29 </when>
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30 </conditional>
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31 </inputs>
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32
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33 <outputs>
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34 <data name="out_file" format="data_manager_json"/>
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35 </outputs>
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36
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37 <help>
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38 <![CDATA[
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39 **What it does**
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40
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41
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42 | 1. The tool asks the admin to enter a *species_name* and automatically download the last release of the corresponding gtf annotation file on Ensembl.
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43 |
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44 | 2. The tool calls ALFA.py to generate the alfa indexes from this gtf file.
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45 |
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46 | 3. Resulting indexes are stored in the child directory *alfa_indexes/* of the dir *<galaxy_data_manager_data_path>* defined in *config/galaxy.ini*
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47 |
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48 | 4. Finally, the tool adds the new entry to the table *alfa_indexes.loc*. This .loc file is where the data table *alfa_indexes* points, as defined in *config/shed_tool_data_table.conf.xml*
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49 |
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50 | 5. At the end of the process, when a user will use `alfa`_ , the built-in indexes corresponding to the *species_name* will be available
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51
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52 .. _alfa: https://toolshed.g2.bx.psu.edu/view/charles-bernard/alfa
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53
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54 ]]>
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55 </help>
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56
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57 </tool>
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