Mercurial > repos > matthias > data_manager_dada2

annotate data_manager/dada2_fetcher.xml @ 9:facf9e6c872c draft default tip

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit df2dfeb75f88b326f567cab8df4e6c4a7f2e548c
author matthias
date Tue, 15 Oct 2019 07:20:59 -0400
parents da93e6a3fe23
children
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8
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
matthias
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1 <?xml version="1.0"?>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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2 <tool id="dada_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.7">
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3 <description>Download reference databases</description>
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4 <command detect_errors="exit_code"><![CDATA[
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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5 python '$__tool_directory__/data_manager.py'
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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6 --out '$out_file'
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7 #set dataset = str($db_cond.db_select) + '_' + str($db_cond.version_select)
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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8 --dataset '$dataset'
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9 ]]>
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10 </command>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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11 <inputs>
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12 <conditional name="db_cond">
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13 <param name="db_select" type="select" label="Taxonomic database">
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14 <option value="silva">Silva</option>
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15 <option value="rdp">RDP</option>
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16 <option value="greengenes">GreenGenes</option>
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17 <option value="unite">UNITE Fungi: General Fasta</option>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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18 <!-- UNITE Eukaryotes not yet supported https://github.com/benjjneb/dada2/issues/702 -->
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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19 <option value="RefSeq_RDP">NCBI RefSeq 16S rRNA database supplemented by RDP</option>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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20 <option value="gtdb">GTDB: Genome Taxonomy Database (Bacteria &amp; Archaea)</option>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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21 <option value="hitdb">HitDB (Human InTestinal 16S)</option>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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22 <option value="silva_euk_18S">Silva Eukaryotic 18S</option>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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23 <option value="PR2">Protist Ribosomal Reference database (PR2)</option>
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24 </param>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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25 <when value="silva">
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26 <param name="version_select" type="select" label="Database version">
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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27 <option value="132">132</option>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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28 <option value="128">128</option>
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29 </param>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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30 </when>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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31 <when value="rdp">
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32 <param name="version_select" type="select" label="Database version">
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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33 <option value="16">16</option>
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34 <option value="14">14</option>
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35 </param>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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36 </when>
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37 <when value="greengenes">
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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38 <param name="version_select" type="select" label="Database version">
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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39 <option value="13.84">13.84</option>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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40 </param>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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41 </when>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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42 <when value="unite">
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43 <param name="version_select" type="select" label="Database version">
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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44 <option value="8.0_fungi">release 8.0 for Fungi</option>
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45 <option value="8.0_fungi_singletons">release 8.0 for Fungi including global and 97% singletons</option>
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46 </param>
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47 </when>
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48 <when value="RefSeq_RDP">
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49 <param name="version_select" type="select" label="Database version">
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50 <option value="2018_05">05/2018</option>
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51 </param>
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52 </when>
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53 <when value="gtdb">
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54 <param name="version_select" type="select" label="Database version">
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55 <option value="2018_11">11/2018</option>
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56 </param>
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57 </when>
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58 <when value="hitdb">
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59 <param name="version_select" type="select" label="Database version">
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60 <option value="1">1</option>
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61 </param>
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62 </when>
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63 <when value="silva_euk_18S">
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64 <param name="version_select" type="select" label="Database version">
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65 <option value="132">132</option>
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66 </param>
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67 </when>
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68 <when value="PR2">
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69 <param name="version_select" type="select" label="Database version">
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70 <option value="4.11.1">4.11.1</option>
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71 </param>
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72 </when>
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73 </conditional>
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74 </inputs>
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75 <outputs>
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76 <data name="out_file" format="data_manager_json" />
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77 </outputs>
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78 <tests>
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79 <test>
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matthias
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80 <param name="db_cond|db_select" value="silva"/>
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matthias
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81 <param name="db_cond|version_select" value="132"/>
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matthias
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82 <output name="out_file" file="silva132_json"/>
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matthias
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83 </test>
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84 <test>
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85 <param name="db_cond|db_select" value="rdp"/>
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matthias
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86 <param name="db_cond|version_select" value="16"/>
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87 <output name="out_file" file="rdp16_json"/>
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88 </test>
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89 <test>
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90 <param name="db_cond|db_select" value="greengenes"/>
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91 <param name="db_cond|version_select" value="13.84"/>
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92 <output name="out_file" file="greengenes13.84_json"/>
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93 </test>
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94 <test>
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95 <param name="db_cond|db_select" value="unite"/>
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96 <param name="db_cond|version_select" value="8.0_fungi"/>
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97 <output name="out_file" file="unite8fungi_json"/>
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98 </test>
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99 <test>
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100 <param name="db_cond|db_select" value="unite"/>
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101 <param name="db_cond|version_select" value="8.0_fungi_singletons"/>
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102 <output name="out_file" file="unite8fungisingletons_json"/>
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103 </test>
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104 <test>
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105 <param name="db_cond|db_select" value="RefSeq_RDP"/>
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106 <param name="db_cond|version_select" value="2018_05"/>
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107 <output name="out_file" file="RefSeq_RDP2018_json"/>
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108 </test>
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109 <test>
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110 <param name="db_cond|db_select" value="gtdb"/>
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111 <param name="db_cond|version_select" value="2018_11"/>
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112 <output name="out_file" file="gtdb2018_json"/>
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113 </test>
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114 <test>
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115 <param name="db_cond|db_select" value="hitdb"/>
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116 <param name="db_cond|version_select" value="1"/>
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117 <output name="out_file" file="hitdb1_json"/>
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118 </test>
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119 <test>
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120 <param name="db_cond|db_select" value="silva_euk_18S"/>
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121 <param name="db_cond|version_select" value="132"/>
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122 <output name="out_file" file="silvaeuk132_json"/>
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123 </test>
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124 <test>
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125 <param name="db_cond|db_select" value="PR2"/>
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126 <param name="db_cond|version_select" value="4.11.1"/>
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127 <output name="out_file" file="PR24.11.1_json"/>
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128 </test>
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129 </tests>
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130 <help><![CDATA[
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131 Public Reference databases maintained by the DADA2 project
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132 ..........................................................
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133
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134 The following refrence databases which are describes as maintained by the DADA2 project (https://benjjneb.github.io/dada2/training.html) are available
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135
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136 - Silva (https://www.arb-silva.de/)
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137 - RDP (http://rdp.cme.msu.edu/)
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138 - GreenGenes (http://greengenes.secondgenome.com/)
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139 - UNITE general FASTA (https://unite.ut.ee/repository.php)
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140
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141 While Silva and RDP contain reference databases for taxonomy and species assignment, the greengenes and UNITE databases only contains a reference database for taxonomy assignment.
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142
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143 For the Silva databases check the license information: http://www.arb-silva.de/silva-license-information.
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144
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145 Except for UNITE all reference databases are downloaded from the corresponding zenodo links that are listed on the DADA2 website. The UNITE databases are taken from the links provided on the UNITE website
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146
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147 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html.
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148
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149 Further public Reference databases listed by the DADA2 project
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150 ..............................................................
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151
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152 Several contributed reference databases are listed of the DADA2 project website (https://benjjneb.github.io/dada2/training.html):
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153
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154 - RefSeq + RDP (NCBI RefSeq 16S rRNA database supplemented by RDP)
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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155 - GTDB: Genome Taxonomy Database (More info: http://gtdb.ecogenomic.org/)
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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156 - HitDB version 1 (Human InTestinal 16S rRNA) (https://github.com/microbiome/HITdb)
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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157 - RDP fungi LSU
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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158 - Silva Eukaryotic 18S
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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159 - PR2 (https://github.com/pr2database/pr2database)
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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160
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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161 Except for PR2, all reference databases are downloaded from the corresponding zenodo links that are listed on the DADA2 website. The PR2 database is taken from their github page.
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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162
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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163 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html.
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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164 ]]></help>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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165 <citations>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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166 <!-- silva -->
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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167 <citation type="doi">10.1093/nar/gks1219</citation>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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168 <!-- rdp -->>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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169 <citation type="doi">10.1093/nar/gkt1244</citation>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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170 <!-- greengenes -->
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171 <citation type="doi">10.1128/AEM.03006-05</citation>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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172 <!-- unite -->
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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173 <citation type="doi">10.15156/BIO/786343</citation>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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174 <!-- TODO gtdb ??? -->
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175 <!-- hitdb -->
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176 <citation type="doi">10.1186/s12864-015-2265-y</citation>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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177 <!-- PR2 -->
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178 <citation type="doi">10.1093/nar/gks1160</citation>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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179 </citations>
da93e6a3fe23 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 5d8314337211e041568578b0e85001af05b73c2a
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180 </tool>
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181