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