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1 <tool id="ctat_genome_ref_lib_data_manager"
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2 name="CTAT Genome Reference Library Data Manager"
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3 version="1.0.0" tool_type="manage_data">
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4 <description>Retrieve, and/or Specify the location of, a CTAT Genome Reference Library.
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5 </description>
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6 <requirements>
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7 <requirement type="package" version="2.7">python</requirement>
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8 </requirements>
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9 <command detect_errors="default">
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10 <![CDATA[
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11 python $__tool_directory__/add_ctat_ref_lib.py ${download}
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12 --genome_name "${genome_name}"
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13 --destination_path "${destination}"
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14 --output_filename "${out_file}"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="download" type="boolean" checked="false"
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19 truevalue="--download" falsevalue="" label="Need to Download? (yes/no)" />
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20 <param name="genome_name" type="text" label="Reference Genome name" />
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21 <param name="destination" type="text" label="Local Destination (full path)" />
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22 </inputs>
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23 <outputs>
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24 <data name="out_file" format="data_manager_json" />
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25 </outputs>
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26 <help>
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27 Retrieve, and/or specify the location of, a CTAT Genome Reference Library.
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28 When download is true, the file retrieved and processed is https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v26_CTAT_lib_Nov012017.plug-n-play.tar.gz.
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29 Specify the Full Path of the location where the CTAT Reference Library should be placed.
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30 You will need approximately 30GB of space for this library.
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31 If you already have the library, specify the full path of the location where it exists and leave the download box unchecked.
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32 The Reference Genome name may be left empty if downloading. The name will be used as the selector text of the entry in the data table.
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33 For more information on CTAT Genome Reference Libraries, see <a http="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a>
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34 </help>
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35 </tool> |
