|
0
|
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
|
|
2
|
6 --dbkey_description ${ dbkey.get_display_text() }
|
|
0
|
7
|
|
|
8 ]]></command>
|
|
|
9 <inputs>
|
|
|
10 <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file">
|
|
|
11 <option value="representative">Representative GFF</option>
|
|
|
12 <option value="full">GFF with complete features</option>
|
|
|
13 </param>
|
|
|
14
|
|
2
|
15 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
|
|
0
|
16 <param type="text" name="sequence_name" value="" label="Name of sequence" />
|
|
|
17 <param type="text" name="sequence_id" value="" label="ID for sequence" />
|
|
|
18 <conditional name="reference_source">
|
|
|
19 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
|
|
|
20 <option value="url">URL</option>
|
|
|
21 <option value="history">History</option>
|
|
|
22 <option value="directory">Directory on Server</option>
|
|
|
23 </param>
|
|
|
24 <when value="url">
|
|
|
25 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
|
|
|
26 </when>
|
|
|
27 <when value="history">
|
|
|
28 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
|
|
|
29 </when>
|
|
|
30 <when value="directory">
|
|
|
31 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" />
|
|
|
32 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" />
|
|
|
33 </when>
|
|
|
34 </conditional>
|
|
|
35 </inputs>
|
|
|
36 <outputs>
|
|
|
37 <data name="out_file" format="data_manager_json"/>
|
|
|
38 </outputs>
|
|
|
39 <tests>
|
|
|
40 <!-- TODO: need some way to test that new entry was added to data table -->
|
|
|
41 <test>
|
|
|
42 <param name="dbkey" value="anoGam1"/>
|
|
|
43 <param name="sequence_name" value=""/>
|
|
|
44 <param name="sequence_desc" value=""/>
|
|
|
45 <param name="sequence_id" value=""/>
|
|
|
46 <param name="reference_source_selector" value="history"/>
|
|
|
47 <param name="input_fasta" value="phiX174.fasta"/>
|
|
|
48 <param name="sort_selector" value="as_is"/>
|
|
|
49 <output name="out_file" file="phiX174.data_manager_json"/>
|
|
|
50 </test>
|
|
|
51 </tests>
|
|
|
52 <help>
|
|
|
53 **What it does**
|
|
|
54
|
|
|
55 Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table.
|
|
|
56
|
|
|
57 ------
|
|
|
58
|
|
|
59
|
|
|
60
|
|
|
61 .. class:: infomark
|
|
|
62
|
|
|
63 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
|
|
|
64
|
|
|
65 </help>
|
|
|
66 </tool>
|
