Mercurial > repos > trinity_ctat > ctat_genome_ref_lib_data_manager_test2
comparison data_manager/add_ctat_centrifuge_index.xml @ 15:367b0d693b0c draft default tip
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author | trinity_ctat |
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date | Mon, 30 Apr 2018 16:17:37 -0400 |
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14:3bb91cebec5c | 15:367b0d693b0c |
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1 <tool id="ctat_centrifuge_indexes_data_manager" | |
2 name="CTAT Centrifuge Indexes Data Manager" | |
3 version="1.0.0" tool_type="manage_data"> | |
4 <description>Retrieve, and/or specify the location of, a CTAT Centrifuge Index. | |
5 </description> | |
6 <requirements> | |
7 <requirement type="package" version="2.7">python</requirement> | |
8 </requirements> | |
9 <command detect_errors="default"> | |
10 <![CDATA[ | |
11 python $__tool_directory__/add_ctat_centrifuge_index.py | |
12 --display_name "${display_name}" | |
13 --destination_path "${destination}" | |
14 --output_filename "${out_file}" | |
15 #if str( $download_question.download ) == "true": | |
16 --download_location "\"${download_question.filename}\"" | |
17 #if str( $download_question.force_download ) == "true": | |
18 --force_download | |
19 #end if | |
20 #end if | |
21 ]]> | |
22 </command> | |
23 <inputs> | |
24 <!-- The following are left in here, just as examples of various ways of doing options. | |
25 <param name="force_download" type="boolean" checked="false" | |
26 truevalue="- -force_download" falsevalue="" label="Force New Download? (yes/no)" /> | |
27 <param name="download" type="select" label="Need to Download?"> | |
28 <option value="single" selected="true">Single Dataset</option> | |
29 <option value="paired_collection">Paired Collection</option> | |
30 <when value="paired_collection"> | |
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"/> | |
32 </when> | |
33 --> | |
34 <conditional name="download_question"> | |
35 <param name="download" type="boolean" checked="false" label="Need to Download?" /> | |
36 <when value="true"> | |
37 <!-- The use of a code block to get dynamic options is now deprecated and discouraged. | |
38 I am still using it here. The only other way I can think of to do this is to | |
39 create another data_manager that gets the list of files and puts them into a | |
40 data_table, that is then used to get the filenames. That would require the admin | |
41 to first run the data_manager that builds the filename data_table before running | |
42 this data_manager. | |
43 However, I have not been able to figure out how to send information back correctly | |
44 from the function and there is no documentation that I have found showing how to do it. | |
45 <param name="filename" type="select" label="Select File" display="radio" | |
46 dynamic_options="get_ctat_centrifuge_index_locations()" | |
47 help="Select a Centrifuge Index to Download." /> | |
48 Hard coded version. | |
49 <param name="filename" type="text" value="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz"> | |
50 <option value="ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz"> | |
51 p_compressed+h+v | |
52 </option> | |
53 </param> | |
54 --> | |
55 <param name="filename" type="select" label="Select File" | |
56 dynamic_options="get_ctat_centrifuge_index_locations()" | |
57 help="Select a Centrifuge Index to Download." /> | |
58 <param name="force_download" type="boolean" checked="false" label="Force New Download?" /> | |
59 </when> | |
60 </conditional> | |
61 | |
62 <param name="display_name" type="text" label="Centrifuge Index Display Name" /> | |
63 <param name="destination" type="text" label="Local Destination (full path)" /> | |
64 </inputs> | |
65 <outputs> | |
66 <data name="out_file" format="data_manager_json" /> | |
67 </outputs> | |
68 <help> | |
69 Retrieve, and/or specify the location of, a CTAT Centrifuge Index. | |
70 When download is true, the file at ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz | |
71 will be the URL from which the index is downloaded. Currently that is the only supported index. | |
72 Specify the Full Path of the destination where the CTAT Reference Library should be placed. | |
73 If you already have the index, specify the full path of the location where it exists and leave the download box unchecked. | |
74 The display_name may be left empty if downloading. | |
75 The display_name will be used as the selector text of the entry in the data table. | |
76 </help> | |
77 <code file="add_ctat_centrifuge_index.py" /> | |
78 </tool> |