0
|
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>
|