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1 <tool id="diamond_database_builder" name="Diamond" tool_type="manage_data" version="0.0.1">
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2 <description> Database builder</description>
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3 <requirements>
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4 <requirement type="package" version="0.6.13">diamond</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 data_manager_diamond_database_builder.py "${out_file}"
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8 </command>
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9 <inputs>
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10 <param type="text" name="database_name" value="" label="Database name or description"
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11 help="This will be shown to the user in the database selectbox."/>
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12 <param type="text" name="database_id" value="" label="Database ID" help="This needs to be unique. No whitespaces allowed. Use underscores." />
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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="ncbi">NCBI</option>
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16 <option value="url">URL</option>
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17 <option value="history" selected="True" help="Recommended to archive the original FASTA file as well.">History</option>
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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="ncbi">
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21 <param type="text" name="requested_identifier" value="" label="NCBI identifier" help="e.g. nr" optional="False" />
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22 </when>
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23 <when value="url">
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24 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
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25 </when>
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26 <when value="history">
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27 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
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28 </when>
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29 <when value="directory">
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30 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
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31 <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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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data name="out_file" format="data_manager_json"/>
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37 </outputs>
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38 <help>
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39
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40 .. class:: infomark
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41
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42 NCBI databases can be downded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
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43 For example the NR database can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
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44
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45 </help>
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46 </tool>
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