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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
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3
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4 <requirements>
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5 <requirement type="package" version="0.1.0">alfa</requirement>
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6 </requirements>
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7
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8 <command interpreter="python">data_manager_build_alfa_indexes.py -e "${reference_source['kingdom']}" "${reference_source['species_name']}" -o "${out_file}" $__root_dir__ </command>
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3
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9
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10 <inputs>
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11 <conditional name="reference_source">
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12 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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13 <option value="ensembl" selected="True">Ensembl Genomes Websites</option>
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14 </param>
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15 <when value="ensembl">
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16 <param name="kingdom" type="select" label="Select the ensembl website where to fetch the genome">
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17 <option value="vertebrates" selected="True">Ensembl (Vertebrates)</option>
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18 <option value="bacteria" selected="True">Ensembl Bacteria</option>
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19 <option value="fungi" selected="True">Ensembl Fungi</option>
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20 <option value="metazoa" selected="True">Ensembl Metazoa</option>
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21 <option value="plants" selected="True">Ensembl Plants</option>
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22 <option value="protists" selected="True">Ensembl Protists</option>
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23 </param>
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24 <param name="species_name" type="text" value="Homo sapiens" label="Complete Species_Name" optional="False">
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25 <validator type="empty_field" message="Please, enter a species name."/>
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26 </param>
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27 </when>
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28 </conditional>
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29 </inputs>
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30
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31 <outputs>
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32 <data name="out_file" format="data_manager_json"/>
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33 </outputs>
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34 </tool>
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