Mercurial > repos > ieguinoa > data_manager_fetch_gff
comparison data_manager/data_manager_fetch_gff.xml @ 0:ac4fde07eaed draft
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author | ieguinoa |
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date | Mon, 09 Jul 2018 11:58:50 -0400 |
parents | |
children | c57bd7f3fb46 |
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1 <tool id="data_manager_fetch_gff" name="Create entries in gff data table" version="0.0.1" tool_type="manage_data"> | |
2 <description>fetching</description> | |
3 <command><![CDATA[ | |
4 python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}" | |
5 --type $file_type | |
6 #if str( $dbkey_source.dbkey_source_selector ) == 'existing': | |
7 --dbkey_description ${ dbkey_source.dbkey.get_display_text() } | |
8 #else | |
9 --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" | |
10 #end if | |
11 | |
12 ]]></command> | |
13 <inputs> | |
14 <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file"> | |
15 <option value="representative">Representative GFF</option> | |
16 <option value="full">GFF with complete features</option> | |
17 </param> | |
18 | |
19 <conditional name="dbkey_source"> | |
20 <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> | |
21 <option value="existing" selected="True">Existing</option> | |
22 <option value="new">New</option> | |
23 </param> | |
24 <when value="existing"> | |
25 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> | |
26 </when> | |
27 <when value="new"> | |
28 <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> | |
29 <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> | |
30 </when> | |
31 </conditional> | |
32 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
33 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
34 <conditional name="reference_source"> | |
35 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
36 <option value="url">URL</option> | |
37 <option value="history">History</option> | |
38 <option value="directory">Directory on Server</option> | |
39 </param> | |
40 <when value="url"> | |
41 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> | |
42 </when> | |
43 <when value="history"> | |
44 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> | |
45 </when> | |
46 <when value="directory"> | |
47 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> | |
48 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" /> | |
49 </when> | |
50 </conditional> | |
51 </inputs> | |
52 <outputs> | |
53 <data name="out_file" format="data_manager_json"/> | |
54 </outputs> | |
55 <tests> | |
56 <!-- TODO: need some way to test that new entry was added to data table --> | |
57 <test> | |
58 <param name="dbkey" value="anoGam1"/> | |
59 <param name="sequence_name" value=""/> | |
60 <param name="sequence_desc" value=""/> | |
61 <param name="sequence_id" value=""/> | |
62 <param name="reference_source_selector" value="history"/> | |
63 <param name="input_fasta" value="phiX174.fasta"/> | |
64 <param name="sort_selector" value="as_is"/> | |
65 <output name="out_file" file="phiX174.data_manager_json"/> | |
66 </test> | |
67 </tests> | |
68 <help> | |
69 **What it does** | |
70 | |
71 Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table. | |
72 | |
73 ------ | |
74 | |
75 | |
76 | |
77 .. class:: infomark | |
78 | |
79 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
80 | |
81 </help> | |
82 </tool> |