Mercurial > repos > thanhlv > data_manager_build_ariba_database

annotate data_manager/ariba_database_builder.xml @ 7:8a442938a61a draft

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planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 98648bbb7796db528b5685d44a2a5b761c53c19b-dirty
author thanhlv
date Sun, 19 May 2019 08:50:27 -0400
parents 6286fb2cadf5
children fb4da292b6d0
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1 <?xml version="1.0"?>
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2 <tool id="ariba_database_builder" name="ARIBA" tool_type="manage_data" version="@VERSION@">
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3 <description>database builder</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <version_command>ariba version | head head -n 1</version_command>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 #if str($library.lib_type) != "fasta"
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12 python '$__tool_directory__/ariba_data_base_builder.py' '${out_file}' -t $library.lib_type -d $library.db
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13 #else
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14 python '$__tool_directory__/ariba_data_base_builder.py' '${out_file}' -t $library.lib_type -d $library.db -c $library.coding -f $library.fasta
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15 #end if
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16 ]]>
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17 </command>
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18 <inputs>
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19 <conditional name="library">
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20 <param name="lib_type" type="select" label="Input reads type or collection" help="Select a curated database or a fasta from the history">
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21 <option value="curated" selected="true">Curated Database</option>
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22 <option value="mlst" selected="true">MLST</option>
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23 <option value="fasta">A fasta file</option>
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24 </param>
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25 <when value="curated">
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26 <param name="db" type="select" multiple="false" label="Select partial library to download">
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27 <option value="card">CARD</option>
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28 <option value="resfinder">Resfinder</option>
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29 <option value="plasmidfinder">Plasmidfinder</option>
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30 <option value="megares">Megares</option>
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31 <option value="argannot">Argannot</option>
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32 <option value="vfdb_core">vfdb_core</option>
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33 <option value="vfdb_full">vfdb_full</option>
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34 <option value="virulencefinder">virulencefinder</option>
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35 </param>
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36 <when value="mlst">
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37 <param name="db" type="select" multiple="false" label="Select a species">
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38 <option value="achs">Achromobacter spp.</option>
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39 <option value="acib1">Acinetobacter baumannii#1</option>
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40 <option value="acib2">Acinetobacter baumannii#2</option>
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41 <option value="aers">Aeromonas spp.</option>
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42 <option value="anap">Anaplasma phagocytophilum</option>
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43 <option value="arcs">Arcobacter spp.</option>
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44 <option value="aspf">Aspergillus fumigatus</option>
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45 <option value="bacc">Bacillus cereus</option>
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46 <option value="bacl">Bacillus licheniformis</option>
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47 <option value="bacs">Bacillus subtilis</option>
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48 <option value="barb">Bartonella bacilliformis</option>
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49 <option value="barh">Bartonella henselae</option>
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50 <option value="bors">Bordetella spp.</option>
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51 <option value="borr">Borrelia spp.</option>
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52 <option value="brah">Brachyspira hampsonii</option>
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53 <option value="brach">Brachyspira hyodysenteriae</option>
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54 <option value="brai">Brachyspira intermedia</option>
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55 <option value="brap">Brachyspira pilosicoli</option>
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56 <option value="bras">Brachyspira spp.</option>
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57 <option value="brus">Brucella spp.</option>
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58 <option value="bucc">Burkholderia cepacia complex</option>
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59 <option value="burp">Burkholderia pseudomallei</option>
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60 <option value="camc">Campylobacter concisus/curvus</option>
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61 <option value="camf">Campylobacter fetus</option>
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62 <option value="camh">Campylobacter helveticus</option>
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63 <option value="rlis">Campylobacter hyointestinalis</option>
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64 <option value="cami">Campylobacter insulaenigrae</option>
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65 <option value="camj">Campylobacter jejuni</option>
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66 <option value="caml">Campylobacter lanienae</option>
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67 <option value="rari">Campylobacter lari</option>
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68 <option value="cams">Campylobacter sputorum</option>
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69 <option value="camu">Campylobacter upsaliensis</option>
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70 <option value="cana">Candida albicans</option>
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71 <option value="cang">Candida glabrata</option>
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72 <option value="cank">Candida krusei</option>
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73 <option value="cant">Candida tropicalis</option>
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74 <option value="cals">Candidatus Liberibacter solanacearum</option>
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75 <option value="carm">Carnobacterium maltaromaticum</option>
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76 <option value="chls">Chlamydiales spp.</option>
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77 <option value="citf">Citrobacter freundii</option>
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78 <option value="clos">Clonorchis sinensis</option>
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79 <option value="clob">Clostridium botulinum</option>
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80 <option value="clod">Clostridium difficile</option>
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81 <option value="mcum">Clostridium septicum</option>
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82 <option value="cord">Corynebacterium diphtheriae</option>
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83 <option value="cros">Cronobacter spp.</option>
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84 <option value="dicn">Dichelobacter nodosus</option>
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85 <option value="edws">Edwardsiella spp.</option>
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86 <option value="entc">Enterobacter cloacae</option>
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87 <option value="entf">Enterococcus faecalis</option>
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88 <option value="sium">Enterococcus faecium</option>
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89 <option value="escc1">Escherichia coli#1</option>
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90 <option value="escc2">Escherichia coli#2</option>
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91 <option value="flap">Flavobacterium psychrophilum</option>
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92 <option value="gala">Gallibacterium anatis</option>
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93 <option value="haei">Haemophilus influenzae</option>
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94 <option value="haep">Haemophilus parasuis</option>
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95 <option value="helc">Helicobacter cinaedi</option>
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96 <option value="help">Helicobacter pylori</option>
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97 <option value="hels">Helicobacter suis</option>
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98 <option value="kink">Kingella kingae</option>
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99 <option value="klea">Klebsiella aerogenes</option>
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100 <option value="kleo">Klebsiella oxytoca</option>
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101 <option value="klep">Klebsiella pneumoniae</option>
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102 <option value="kuds">Kudoa septempunctata</option>
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103 <option value="lacs">Lactobacillus salivarius</option>
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104 <option value="leps">Leptospira spp.</option>
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105 <option value="leps2">Leptospira spp.#2</option>
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106 <option value="leps3">Leptospira spp.#3</option>
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107 <option value="lism">Listeria monocytogenes</option>
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108 <option value="macc">Macrococcus canis</option>
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109 <option value="scus">Macrococcus caseolyticus</option>
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110 <option value="manh">Mannheimia haemolytica</option>
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111 <option value="melp">Melissococcus plutonius</option>
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112 <option value="morc">Moraxella catarrhalis</option>
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113 <option value="mycs">Mycobacteria spp.</option>
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114 <option value="myca">Mycobacterium abscessus</option>
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115 <option value="mycm">Mycobacterium massiliense</option>
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116 <option value="mycoa">Mycoplasma agalactiae</option>
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117 <option value="mycb">Mycoplasma bovis</option>
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118 <option value="mych">Mycoplasma hyopneumoniae</option>
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119 <option value="anis">Mycoplasma hyorhinis</option>
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120 <option value="myci">Mycoplasma iowae</option>
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121 <option value="mycp">Mycoplasma pneumoniae</option>
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122 <option value="mycos">Mycoplasma synoviae</option>
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123 <option value="neis">Neisseria spp.</option>
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124 <option value="orit">Orientia tsutsugamushi</option>
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125 <option value="ornr">Ornithobacterium rhinotracheale</option>
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126 <option value="pael">Paenibacillus larvae</option>
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127 <option value="pasm1">Pasteurella multocida#1</option>
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128 <option value="pasm2">Pasteurella multocida#2</option>
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129 <option value="pedp">Pediococcus pentosaceus</option>
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130 <option value="phod">Photobacterium damselae</option>
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131 <option value="piss">Piscirickettsia salmonis</option>
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132 <option value="porg">Porphyromonas gingivalis</option>
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133 <option value="proa">Propionibacterium acnes</option>
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134 <option value="psea">Pseudomonas aeruginosa</option>
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135 <option value="psef">Pseudomonas fluorescens</option>
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136 <option value="psep">Pseudomonas putida</option>
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137 <option value="rhos">Rhodococcus spp.</option>
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138 <option value="riea">Riemerella anatipestifer</option>
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139 <option value="sale">Salmonella enterica</option>
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140 <option value="sapp">Saprolegnia parasitica</option>
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141 <option value="sins">Sinorhizobium spp.</option>
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142 <option value="staa">Staphylococcus aureus</option>
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143 <option value="stae">Staphylococcus epidermidis</option>
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144 <option value="stah">Staphylococcus haemolyticus</option>
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145 <option value="snis">Staphylococcus hominis</option>
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146 <option value="stal">Staphylococcus lugdunensis</option>
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147 <option value="stap">Staphylococcus pseudintermedius</option>
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148 <option value="stem">Stenotrophomonas maltophilia</option>
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149 <option value="stra">Streptococcus agalactiae</option>
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150 <option value="sbcx">Streptococcus bovis/equinus complex (SBSEC)</option>
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151 <option value="strc">Streptococcus canis</option>
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152 <option value="stde">Streptococcus dysgalactiae equisimilis</option>
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153 <option value="strg">Streptococcus gallolyticus</option>
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154 <option value="stro">Streptococcus oralis</option>
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155 <option value="strp">Streptococcus pneumoniae</option>
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156 <option value="snes">Streptococcus pyogenes</option>
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157 <option value="strs">Streptococcus suis</option>
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158 <option value="strt">Streptococcus thermophilus</option>
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159 <option value="strt2">Streptococcus thermophilus#2</option>
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160 <option value="stru">Streptococcus uberis</option>
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161 <option value="strz">Streptococcus zooepidemicus</option>
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162 <option value="sspp">Streptomyces spp</option>
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163 <option value="tays">Taylorella spp.</option>
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164 <option value="tens">Tenacibaculum spp.</option>
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165 <option value="trep">Treponema pallidum</option>
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166 <option value="triv">Trichomonas vaginalis</option>
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167 <option value="ures">Ureaplasma spp.</option>
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168 <option value="vibc">Vibrio cholerae</option>
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169 <option value="vibc2">Vibrio cholerae#2</option>
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170 <option value="vibp">Vibrio parahaemolyticus</option>
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171 <option value="vibs">Vibrio spp.</option>
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172 <option value="vibt">Vibrio tapetis</option>
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173 <option value="vibv">Vibrio vulnificus</option>
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174 <option value="wolb">Wolbachia</option>
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175 <option value="xylf">Xylella fastidiosa</option>
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176 <option value="yerp">Yersinia pseudotuberculosis</option>
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177 <option value="yerr">Yersinia ruckeri</option>
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178 <option value="yers">Yersinia spp.</option>
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179 </param>
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180 </when>
0
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181 </when>
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182 <when value="fasta">
4
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183 <param name="fasta" type="data" format="fasta,fasta.gz" optional="false" />
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184 <param name="db" type="text" label="DB name" help = "The DB name should include no space, special characters, and must be uniquely different to the name predefined in curated and mlst list" />
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185 <param name="coding" type="boolean" truevalue="yes" falsevalue="no" checked="False" label="Coding sequence?" />
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186 </when>
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187 </conditional>
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188 </inputs>
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189 <outputs>
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190 <data name="out_file" format="data_manager_json" />
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191 </outputs>
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192 <help>
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193 </help>
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194 <citations>
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195 <citation type="doi">110.1099/mgen.0.000131</citation>
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196 </citations>
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197 </tool>