Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
comparison data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 3:86fa71e9b427 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
author | devteam |
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date | Fri, 26 Aug 2016 12:46:47 -0400 |
parents | 776bb1b478a0 |
children | 60994ca04177 |
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2:776bb1b478a0 | 3:86fa71e9b427 |
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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"> | 1 <tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.2" tool_type="manage_data"> |
2 <description>fetching</description> | 2 <description>fetching</description> |
3 <command interpreter="python">data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" | 3 <command><![CDATA[ |
4 #if str( $dbkey_source.dbkey_source_selector ) == 'existing': | 4 python "$__tool_directory__"/data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" |
5 --dbkey_description ${ dbkey_source.dbkey.get_display_text() } | 5 #if str( $dbkey_source.dbkey_source_selector ) == 'existing': |
6 #else | 6 --dbkey_description ${ dbkey_source.dbkey.get_display_text() } |
7 --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" | 7 #else |
8 #end if | 8 --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" |
9 | 9 #end if |
10 </command> | 10 ]]></command> |
11 <inputs> | 11 <inputs> |
12 <conditional name="dbkey_source"> | 12 <conditional name="dbkey_source"> |
13 <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> | 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> | 14 <option value="existing" selected="True">Existing</option> |
15 <option value="new">New</option> | 15 <option value="new">New</option> |
16 </param> | 16 </param> |
17 <when value="existing"> | 17 <when value="existing"> |
18 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> | 18 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> |
19 </when> | 19 </when> |
20 <when value="new"> | 20 <when value="new"> |
21 <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> | 21 <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> |
22 <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> | 22 <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> |
23 </when> | 23 </when> |
24 </conditional> | 24 </conditional> |
25 | |
26 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | 25 <param type="text" name="sequence_name" value="" label="Name of sequence" /> |
27 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | 26 <param type="text" name="sequence_id" value="" label="ID for sequence" /> |
28 <conditional name="reference_source"> | 27 <conditional name="reference_source"> |
29 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | 28 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
30 <option value="ucsc" selected="True">UCSC</option> | 29 <option value="ucsc" selected="True">UCSC</option> |
31 <option value="ncbi">NCBI</option> | 30 <option value="ncbi">NCBI</option> |
32 <option value="url">URL</option> | 31 <option value="url">URL</option> |
33 <option value="history">History</option> | 32 <option value="history">History</option> |
34 <option value="directory">Directory on Server</option> | 33 <option value="directory">Directory on Server</option> |
35 </param> | 34 </param> |
36 <when value="ucsc"> | 35 <when value="ucsc"> |
37 <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> | 36 <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> |
38 </when> | 37 </when> |
39 <when value="ncbi"> | 38 <when value="ncbi"> |
40 <param type="text" name="requested_identifier" value="" label="NCBI identifier" optional="False" /> | 39 <param type="text" name="requested_identifier" value="" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" optional="False" /> |
41 </when> | 40 </when> |
42 <when value="url"> | 41 <when value="url"> |
43 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> | 42 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> |
44 </when> | 43 </when> |
45 <when value="history"> | 44 <when value="history"> |
46 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> | 45 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> |
47 </when> | 46 </when> |
48 <when value="directory"> | 47 <when value="directory"> |
49 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> | 48 <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" /> | 49 <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> | 50 </when> |
52 </conditional> | 51 </conditional> |
53 <conditional name="sorting"> | 52 <conditional name="sorting"> |
54 <param name="sort_selector" type="select" label="Sort by chromosome name"> | 53 <param name="sort_selector" type="select" label="Sort by chromosome name"> |
55 <option value="as_is" selected="True">As is</option> | 54 <option value="as_is" selected="True">As is</option> |
56 <option value="lexicographical">Lexicographical</option> | 55 <option value="lexicographical">Lexicographical</option> |
57 <option value="gatk">GATK</option> | 56 <option value="gatk">GATK</option> |
58 <option value="custom">Custom</option> | 57 <option value="custom">Custom</option> |
59 </param> | 58 </param> |
60 <when value="as_is"> | 59 <when value="as_is"> |
61 </when> | 60 </when> |
62 <when value="lexicographical"> | 61 <when value="lexicographical"> |
63 </when> | 62 </when> |
64 <when value="gatk"> | 63 <when value="gatk"> |
65 </when> | 64 </when> |
66 <when value="custom"> | 65 <when value="custom"> |
67 <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> | 66 <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> |
68 <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" /> | 67 <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" /> |
69 </repeat> | 68 </repeat> |
70 <conditional name="handle_not_listed"> | |
71 <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> | 69 <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> |
72 <option value="discard" selected="True">Discard</option> | 70 <option value="discard" selected="True">Discard</option> |
73 <option value="keep_append">Keep and Append</option> | 71 <option value="keep_append">Keep and Append</option> |
74 <option value="keep_prepend">Keep and Prepend</option> | 72 <option value="keep_prepend">Keep and Prepend</option> |
75 </param> | 73 </param> |
76 <when value="discard"> | 74 </when> |
77 </when> | |
78 <when value="keep_append"> | |
79 </when> | |
80 <when value="keep_prepend"> | |
81 </when> | |
82 </conditional> | |
83 </when> | |
84 </conditional> | 75 </conditional> |
85 </inputs> | 76 </inputs> |
86 <outputs> | 77 <outputs> |
87 <data name="out_file" format="data_manager_json"/> | 78 <data name="out_file" format="data_manager_json"/> |
88 </outputs> | 79 </outputs> |
108 | 99 |
109 | 100 |
110 | 101 |
111 .. class:: infomark | 102 .. class:: infomark |
112 | 103 |
113 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | 104 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
114 | 105 |
115 </help> | 106 </help> |
116 </tool> | 107 </tool> |