Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta

comparison data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 3:86fa71e9b427 draft

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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
date Fri, 26 Aug 2016 12:46:47 -0400
parents 776bb1b478a0
children 60994ca04177
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2:776bb1b478a0 3:86fa71e9b427
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>