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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 <requirement type="package" version="0.3.0">gmap-fusion</requirement>
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9 <!-- gmap-fusion is required in order to process downloaded libraries
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10 to create all of the required files and indexes. It includes gmap
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11 and FusionFilter, programs from both of which are needed.
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12 -->
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13 </requirements>
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14 <command detect_errors="default">
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15 <![CDATA[
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16 python $__tool_directory__/add_ctat_ref_lib.py
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17 --genome_name "${genome_name}"
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18 --destination_path "${destination}"
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19 --output_filename "${out_file}"
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20 #if str(${download}) == "true":
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21 --download "${filename}"
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22 #end if
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23 ]]>
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24 </command>
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25 <inputs>
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26 <!--
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27 <param name="download" type="boolean" checked="false"
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28 truevalue="- -download" falsevalue="" label="Need to Download? (yes/no)" />
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29 <param name="download" type="select" label="Need to Download?">
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30 <option value="single" selected="true">Single Dataset</option>
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31 <option value="paired_collection">Paired Collection</option>
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32 <when value="paired_collection">
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33 <param name="fastq_input" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
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34 </when>
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35 -->
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36 <conditional name="download_question">
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37 <param name="download" type="boolean" checked="false" label="Need to Download? (yes/no)" />
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38 </param>
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39 <when value="true">
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40 <param name="filename" type="select" label="Select File" display="radio"
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41 dynamic_options="get_ctat_genome_filenames()" help="Select a CTAT Genome Reference Library to Download." />
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42 </when>
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43 </conditional>
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44
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45 <param name="genome_name" type="text" label="Reference Genome name" />
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46 <param name="destination" type="text" label="Local Destination (full path)" />
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47 </inputs>
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48 <outputs>
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49 <data name="out_file" format="data_manager_json" />
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50 </outputs>
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51 <help>
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52 Retrieve, and/or specify the location of, a CTAT Genome Reference Library.
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53 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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54 Specify the Full Path of the location where the CTAT Reference Library should be placed.
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55 You will need approximately 30GB of space for this library.
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56 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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57 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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58 For more information on CTAT Genome Reference Libraries, see <a http="https://github.com/FusionFilter/FusionFilter/wiki">FusionFilter</a>
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59 </help>
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60 <code file="add_ctat_ref_lib.py"
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61 </tool>
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