Mercurial > repos > ieguinoa > data_manager_fetch_tx2gene
comparison data_manager/data_manager_fetch_tx2gene.xml @ 0:a4d4da89aae1 draft
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author | ieguinoa |
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date | Wed, 10 Oct 2018 05:44:36 -0400 |
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children | 7d3ffe28ff3f |
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-1:000000000000 | 0:a4d4da89aae1 |
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1 <tool id="data_manager_fetch_gff" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data"> | |
2 <description>fetching</description> | |
3 <command><![CDATA[ | |
4 python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}" | |
5 --type $file_type | |
6 --dbkey_description ${ dbkey.get_display_text() } | |
7 --base_dir $__tool_directory__ | |
8 | |
9 ]]></command> | |
10 <inputs> | |
11 | |
12 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> | |
13 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
14 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
15 | |
16 <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)"> | |
17 <option value="gff_gtf">GFF/GTF file</option> | |
18 <option value="tx2gene">tx2gene</option> | |
19 </param> | |
20 <conditional name="reference_source"> | |
21 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
22 <option value="url">URL</option> | |
23 <option value="history">History</option> | |
24 <option value="directory">Directory on Server</option> | |
25 </param> | |
26 <when value="url"> | |
27 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> | |
28 </when> | |
29 <when value="history"> | |
30 <param name="input_fasta" type="data" label="File from History" multiple="False" optional="False" /> | |
31 </when> | |
32 <when value="directory"> | |
33 <param type="text" name="filename" value="" label="Full path to File on disk" optional="False" /> | |
34 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" /> | |
35 </when> | |
36 </conditional> | |
37 </inputs> | |
38 <outputs> | |
39 <data name="out_file" format="data_manager_json"/> | |
40 </outputs> | |
41 <tests> | |
42 <!-- TODO: need some way to test that new entry was added to data table --> | |
43 <test> | |
44 <param name="dbkey" value="anoGam1"/> | |
45 <param name="sequence_name" value=""/> | |
46 <param name="sequence_desc" value=""/> | |
47 <param name="sequence_id" value=""/> | |
48 <param name="reference_source_selector" value="history"/> | |
49 <param name="input_fasta" value="phiX174.fasta"/> | |
50 <param name="sort_selector" value="as_is"/> | |
51 <output name="out_file" file="phiX174.data_manager_json"/> | |
52 </test> | |
53 </tests> | |
54 <help> | |
55 **What it does** | |
56 | |
57 Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table. | |
58 | |
59 ------ | |
60 | |
61 | |
62 | |
63 .. class:: infomark | |
64 | |
65 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
66 | |
67 </help> | |
68 </tool> |