Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
comparison data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 0:c669787306ae draft
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author | devteam |
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date | Tue, 03 Feb 2015 10:08:46 -0500 |
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children | 776bb1b478a0 |
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1 <tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.1" tool_type="manage_data"> | |
2 <description>fetching</description> | |
3 <command interpreter="python">data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" | |
4 #if str( $dbkey_source.dbkey_source_selector ) == 'existing': | |
5 --dbkey_description ${ dbkey_source.dbkey.get_display_text() } | |
6 #else | |
7 --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" | |
8 #end if | |
9 | |
10 </command> | |
11 <inputs> | |
12 <conditional name="dbkey_source"> | |
13 <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> | |
14 <option value="existing" selected="True">Existing</option> | |
15 <option value="new">New</option> | |
16 </param> | |
17 <when value="existing"> | |
18 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> | |
19 </when> | |
20 <when value="new"> | |
21 <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> | |
22 <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> | |
23 </when> | |
24 </conditional> | |
25 | |
26 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
27 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
28 <conditional name="reference_source"> | |
29 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
30 <option value="ucsc" selected="True">UCSC</option> | |
31 <option value="ncbi">NCBI</option> | |
32 <option value="url">URL</option> | |
33 <option value="history">History</option> | |
34 <option value="directory">Directory on Server</option> | |
35 </param> | |
36 <when value="ucsc"> | |
37 <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> | |
38 </when> | |
39 <when value="ncbi"> | |
40 <param type="text" name="requested_identifier" value="" label="NCBI identifier" optional="False" /> | |
41 </when> | |
42 <when value="url"> | |
43 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> | |
44 </when> | |
45 <when value="history"> | |
46 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> | |
47 </when> | |
48 <when value="directory"> | |
49 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> | |
50 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" /> | |
51 </when> | |
52 </conditional> | |
53 <conditional name="sorting"> | |
54 <param name="sort_selector" type="select" label="Choose the source for the reference genome"> | |
55 <option value="as_is" selected="True">As is</option> | |
56 <option value="lexicographical">Lexicographical</option> | |
57 <option value="gatk">GATK</option> | |
58 <option value="custom">Custom</option> | |
59 </param> | |
60 <when value="as_is"> | |
61 </when> | |
62 <when value="lexicographical"> | |
63 </when> | |
64 <when value="gatk"> | |
65 </when> | |
66 <when value="custom"> | |
67 <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> | |
68 <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" /> | |
69 </repeat> | |
70 <conditional name="handle_not_listed"> | |
71 <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> | |
72 <option value="discard" selected="True">Discard</option> | |
73 <option value="keep_append">Keep and Append</option> | |
74 <option value="keep_prepend">Keep and Prepend</option> | |
75 </param> | |
76 <when value="discard"> | |
77 </when> | |
78 <when value="keep_append"> | |
79 </when> | |
80 <when value="keep_prepend"> | |
81 </when> | |
82 </conditional> | |
83 </when> | |
84 </conditional> | |
85 </inputs> | |
86 <outputs> | |
87 <data name="out_file" format="data_manager_json"/> | |
88 </outputs> | |
89 <tests> | |
90 <!-- TODO: need some way to test that new entry was added to data table --> | |
91 <test> | |
92 <param name="dbkey" value="anoGam1"/> | |
93 <param name="sequence_name" value=""/> | |
94 <param name="sequence_desc" value=""/> | |
95 <param name="sequence_id" value=""/> | |
96 <param name="reference_source_selector" value="history"/> | |
97 <param name="input_fasta" value="phiX174.fasta"/> | |
98 <param name="sort_selector" value="as_is"/> | |
99 <output name="out_file" file="phiX174.data_manager_json"/> | |
100 </test> | |
101 </tests> | |
102 <help> | |
103 **What it does** | |
104 | |
105 Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table. | |
106 | |
107 ------ | |
108 | |
109 | |
110 | |
111 .. class:: infomark | |
112 | |
113 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
114 | |
115 </help> | |
116 </tool> |