Mercurial > repos > trinity_ctat > ctat_lncrna_annotations_data_manager
comparison data_manager/add_ctat_lncrna_annotations.xml @ 0:a3aa3f9e1702 draft default tip
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author | trinity_ctat |
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date | Mon, 16 Jul 2018 20:42:55 -0400 |
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-1:000000000000 | 0:a3aa3f9e1702 |
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1 <tool id="ctat_lncrna_annotations_data_manager" | |
2 name="CTAT lncrna annotations Data Manager" | |
3 version="1.0.0" tool_type="manage_data"> | |
4 <description>Retrieve, and/or specify the location of CTAT lncrna annotations. | |
5 </description> | |
6 <requirements> | |
7 <requirement type="package" version="2.7">python</requirement> | |
8 </requirements> | |
9 <command detect_errors="default"> | |
10 <![CDATA[ | |
11 python $__tool_directory__/add_ctat_lncrna_annotations.py | |
12 --display_name "${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 <conditional name="download_question"> | |
25 <param name="download" type="boolean" checked="false" label="Need to Download?" /> | |
26 <when value="true"> | |
27 <param name="filename" type="select" label="Select File" | |
28 dynamic_options="get_ctat_lncrna_annotations_locations()" | |
29 help="Select a lncrna annotations to Download." /> | |
30 <param name="force_download" type="boolean" checked="false" label="Force New Download?" /> | |
31 </when> | |
32 </conditional> | |
33 | |
34 <param name="display_name" type="text" label="lncrna annotations Display Name" /> | |
35 <param name="destination" type="text" label="Local Destination (full path)" /> | |
36 </inputs> | |
37 <outputs> | |
38 <data name="out_file" format="data_manager_json" /> | |
39 </outputs> | |
40 <help> | |
41 .. class:: infomark | |
42 | |
43 Retrieve, and/or specify the location of, a CTAT lncrna annotations. | |
44 When download is true, the annotations from this website_ will be downloaded. | |
45 | |
46 Currently mm9,mm10,hg19,hg38 are supported. | |
47 | |
48 .. class:: infomark | |
49 | |
50 Specify the Full Path of the destination where the CTAT lncrna annotations should be placed. | |
51 If you already have the annotations, specify the full path of the location where it exists and leave the download box unchecked. | |
52 | |
53 .. class:: infomark | |
54 | |
55 The display_name may be left empty if downloading. | |
56 The display_name will be used as the selector text of the entry in the data table. | |
57 | |
58 .. _website: https://data.broadinstitute.org/Trinity/CTAT/lncrna/annotations.tar.gz | |
59 </help> | |
60 <code file="add_ctat_lncrna_annotations.py" /> | |
61 </tool> |