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1 <tool id="ctat_centrifuge_indexes_data_manager"
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2 name="CTAT Centrifuge Indexes 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 Centrifuge Index.
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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 $__tool_directory__/add_ctat_centrifuge_index.py
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12 --display_name "${display_name}"
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13 --destination_path "${destination}"
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14 --output_filename "${out_file}"
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15 #if str( $download_question.download ) == "true":
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16 --download_location "\"${download_question.filename}\""
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17 #if str( $download_question.force_download ) == "true":
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18 --force_download
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19 #end if
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20 #end if
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21 ]]>
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22 </command>
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23 <inputs>
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24 <!-- The following are left in here, just as examples of various ways of doing options.
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25 <param name="force_download" type="boolean" checked="false"
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26 truevalue="- -force_download" falsevalue="" label="Force New Download? (yes/no)" />
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27 <param name="download" type="select" label="Need to Download?">
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28 <option value="single" selected="true">Single Dataset</option>
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29 <option value="paired_collection">Paired Collection</option>
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30 <when value="paired_collection">
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31 <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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32 </when>
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33 -->
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34 <conditional name="download_question">
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35 <param name="download" type="boolean" checked="false" label="Need to Download?" />
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36 <when value="true">
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37 <!-- The use of a code block to get dynamic options is now deprecated and discouraged.
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38 I am still using it here. The only other way I can think of to do this is to
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39 create another data_manager that gets the list of files and puts them into a
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40 data_table, that is then used to get the filenames. That would require the admin
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41 to first run the data_manager that builds the filename data_table before running
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42 this data_manager.
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43 However, I have not been able to figure out how to send information back correctly
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44 from the function and there is no documentation that I have found showing how to do it.
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45 <param name="filename" type="select" label="Select File" display="radio"
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46 dynamic_options="get_ctat_centrifuge_index_locations()"
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47 help="Select a Centrifuge Index to Download." />
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48 Hard coded version.
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49 <param name="filename" type="text" value="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz">
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50 <option value="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz">
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51 p_compressed+h+v
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52 </option>
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53 </param>
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54 -->
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55 <param name="filename" type="select" label="Select File"
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56 dynamic_options="get_ctat_centrifuge_index_locations()"
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57 help="Select a Centrifuge Index to Download." />
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58 <param name="force_download" type="boolean" checked="false" label="Force New Download?" />
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59 </when>
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60 </conditional>
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61
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62 <param name="display_name" type="text" label="Centrifuge Index Display Name" />
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63 <param name="destination" type="text" label="Local Destination (full path)" />
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64 </inputs>
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65 <outputs>
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66 <data name="out_file" format="data_manager_json" />
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67 </outputs>
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68 <help>
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69 Retrieve, and/or specify the location of, a CTAT Centrifuge Index.
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70 When download is true, the file at ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz
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71 will be the URL from which the index is downloaded. Currently that is the only supported index.
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72 Specify the Full Path of the destination where the CTAT Reference Library should be placed.
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73 If you already have the index, specify the full path of the location where it exists and leave the download box unchecked.
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74 The display_name may be left empty if downloading.
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75 The display_name will be used as the selector text of the entry in the data table.
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76 </help>
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77 <code file="add_ctat_centrifuge_index.py" />
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78 </tool>
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