Mercurial > repos > devteam > data_manager_fetch_genome_all_fasta
annotate data_manager/data_manager_fetch_genome_all_fasta.xml @ 3:fb744a070bee draft default tip
planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
author | devteam |
---|---|
date | Wed, 26 Aug 2015 12:00:32 -0400 |
parents | 2ebc856bce29 |
children |
rev | line source |
---|---|
0 | 1 <tool id="data_manager_fetch_genome_all_fasta" name="Reference Genome" version="0.0.1" tool_type="manage_data"> |
2 <description>fetching</description> | |
3 <command interpreter="python">data_manager_fetch_genome_all_fasta.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() }</command> | |
4 <inputs> | |
5 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> | |
6 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
7 <param type="text" name="sequence_desc" value="" label="Description of sequence" /> | |
8 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
9 <conditional name="reference_source"> | |
10 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
11 <option value="ucsc" selected="True">UCSC</option> | |
12 <option value="ncbi">NCBI</option> | |
13 <option value="url">URL</option> | |
14 <option value="history">History</option> | |
15 <option value="directory">Directory on Server</option> | |
16 </param> | |
17 <when value="ucsc"> | |
18 <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> | |
19 </when> | |
20 <when value="ncbi"> | |
21 <param type="text" name="requested_identifier" value="" label="NCBI identifier" optional="False" /> | |
22 </when> | |
23 <when value="url"> | |
24 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> | |
25 </when> | |
26 <when value="history"> | |
27 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> | |
28 </when> | |
29 <when value="directory"> | |
30 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> | |
31 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" /> | |
32 </when> | |
33 </conditional> | |
34 <conditional name="sorting"> | |
3
fb744a070bee
planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
devteam
parents:
0
diff
changeset
|
35 <param name="sort_selector" type="select" label="Sort by chromosome name"> |
0 | 36 <option value="as_is" selected="True">As is</option> |
37 <option value="lexicographical">Lexicographical</option> | |
38 <option value="gatk">GATK</option> | |
39 <option value="custom">Custom</option> | |
40 </param> | |
41 <when value="as_is"> | |
42 </when> | |
43 <when value="lexicographical"> | |
44 </when> | |
45 <when value="gatk"> | |
46 </when> | |
47 <when value="custom"> | |
48 <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> | |
49 <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" /> | |
50 </repeat> | |
51 <conditional name="handle_not_listed"> | |
52 <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> | |
53 <option value="discard" selected="True">Discard</option> | |
54 <option value="keep_append">Keep and Append</option> | |
55 <option value="keep_prepend">Keep and Prepend</option> | |
56 </param> | |
57 <when value="discard"> | |
58 </when> | |
59 <when value="keep_append"> | |
60 </when> | |
61 <when value="keep_prepend"> | |
62 </when> | |
63 </conditional> | |
64 </when> | |
65 </conditional> | |
66 </inputs> | |
67 <outputs> | |
68 <data name="out_file" format="data_manager_json"/> | |
69 </outputs> | |
70 <tests> | |
71 <!-- TODO: need some way to test that new entry was added to data table --> | |
72 <test> | |
73 <param name="dbkey" value="anoGam1"/> | |
74 <param name="sequence_name" value=""/> | |
75 <param name="sequence_desc" value=""/> | |
76 <param name="sequence_id" value=""/> | |
77 <param name="reference_source_selector" value="history"/> | |
78 <param name="input_fasta" value="phiX174.fasta"/> | |
79 <param name="sort_selector" value="as_is"/> | |
80 <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/> | |
81 </test> | |
82 </tests> | |
83 <help> | |
84 **What it does** | |
85 | |
86 Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table. | |
87 | |
88 ------ | |
89 | |
90 | |
91 | |
92 .. class:: infomark | |
93 | |
94 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
95 | |
96 </help> | |
97 </tool> |