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1 <tool id="versioned_data" name="Versioned data retrieval" version="0.1.03">
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2 <description>Retrieve versioned sequence files and/or their blast, bowtie, etc. database indexes</description>
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3 <macros>
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4 <token name="@BINARY@">versioned_data.py</token>
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5 <import>bccdc_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command interpreter="python">
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9 #assert $__user__, Exception( 'You must be logged in to use this tool.' )
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10 versioned_data.py
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11 #if $globalRetrievalDate.strip() > ''
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12 -d "$globalRetrievalDate"
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13 #end if
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14 -r
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15 "
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16 #for $v in $versions:
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17 ${v.database},
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18 #for $r in $v.retrieval:
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19 ${r.retrievalId}
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20 #end for
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21 ,
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22 #for $w in $v.workflows:
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23 ${w.workflow}
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24 #end for
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25 |
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26 #end for
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27 "
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28 -o "$log"
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29 -O "$__app__.security.encode_id($log.id)"
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30 --api_info_path "$api_info_path" ##Actually a file path to configfile that holds api key
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31 </command>
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32 <!-- #:$log.hid:$log.id dataset_id -->
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33 <expand macro="stdio" />
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34
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35 <inputs>
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36 <!-- Implement as datepicker? http://www.learnfaceit.org/for-developers/adding-parameter-types-to-tool -->
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37 <param name="globalRetrievalDate" type="text" label="Global retrieval date [YYYY-MM-DD]" help="The recall system will use this date to try to select the appropriate versions below. Leave empty to select current versions." size="25" />
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38
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39 <param name="api_info" display="radio" type="drill_down" label="For user with Galaxy API Key" dynamic_options="vdb_init_tool_user(__trans__)" />
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40
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41 <repeat name="versions" title="Data Source" min="1" max="15">
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42
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43 <param name="database" type="select" label="Data" dynamic_options="vdb_get_databases()" multiple="false" />
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44
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45 <repeat name="retrieval" title="Retrieval" min="0" max="1">
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46 <param name="retrievalId" label="Version date/id" type="select" dynamic_options="vdb_get_versions(database, globalRetrievalDate)"/>
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47 </repeat>
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48
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49 <repeat name="workflows" title="Workflow" min="0" max="5" >
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50 <param name="workflow" type="select" label="Name" dynamic_options="vdb_get_workflows(database)" />
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51 </repeat>
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52
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53 </repeat>
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54
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55 </inputs>
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56
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57 <configfiles>
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58 <configfile name="api_info_path">${__user__.api_keys[0].key}
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59 $api_info
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60 </configfile>
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61 </configfiles>
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62
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63 <outputs>
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64 <data name="log" format="txt" label="Versioned Data Retrieval" />
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65 </outputs>
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66
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67 <code file="versioned_data_form.py" />
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68
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69 <tests>
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70 <test>
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71 <param name="db_type" value="nucl"/>
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72 <!-- ... -->
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73 </test>
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74 </tests>
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75
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76 <help>
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77
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78 .. class:: infomark
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79
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80
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81 **What it does**
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82
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83 This tool retrieves links to current or past versions of fasta or other types of
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84 data from a cache kept in the Galaxy data library called "Versioned Data". It then places
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85 them into one's current history so that subsequent tools can work with that data.
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86
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87 For example, after using this tool to select a version of the NCBI nt database, a blast search can be carried out on it by selecting "BLAST database from your history" from the "Subject database/sequences" field of the NCBI BLAST+ search tool.
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88
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89 You can select one or more files or databases by version date or id. This list
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90 is supplied from the Shared Data > Data Libraries > Versioned Data folder that has
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91 been set up by an administrator.
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92
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93 The Workflows section allows you to select one or more pre-defined workflows
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94 to execute on the versioned data. The results are placed in your history for use
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95 by other tools or workflows.
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96
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97 A caching system exists to cache the versioned data or workflow data that the tool generates.
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98 If you request versioned data or derivative data that isn't cached, it may take time to regenerate.
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99
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100 The top-level "Global retrieval date [YYYY-MM-DD]" field that the form starts with will be applied to
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101 all selected databases. This can be overriden by a retrieval date or version that
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102 you supply for a particular database. Leave it and any "Retrievals" inputs empty if you just need the latest version of selected databases.
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103
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104 -------
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105
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106 .. class:: warningmark
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107
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108 **Note**
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109
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110 Again, some past database versions can take time to regenerate if there is no cached version available, for example NCBI nt is a 50+ gigabyte file that needs to be read through to get a fasta version, and a makeblastdb workflow on top of that can take hours on the first call. Access to cached versions is immediate.
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111
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112 Setup of versioned data sources and workflow options can only be done by a Galaxy administrator.
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113
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114 -------
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115
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116 **References**
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117
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118 If you use this Galaxy tool in work leading to a scientific publication please
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119 cite the following paper:
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120
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121 *Reference coming soon...*
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122
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123 </help>
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124 </tool>
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