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annotate wgmlst_export.xml @ 1:5b2c48fa0175 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
author bvalot
date Wed, 07 Dec 2022 15:25:06 +0000
parents a3cc35af3635
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1
5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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1 <tool id="wgmlst_export_wrapper" name="Export result of cg/wgMLST database"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
0
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3 <description></description>
1
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4 <macros>
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5 <import>macro.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
0
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8 <stdio>
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9 <exit_code range="1:" level="fatal" />
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10 </stdio>
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11 <version_command>wgMLST -v</version_command>
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12 <command>
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13 wgMLST
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14 #if $export_result.export == "distance"
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15 distance
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16 #end if
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17 #if $export_result.export == "mlst"
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18 mlst
1
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19 #if $export_result.mlsttype == "grapetree"
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20 -f grapetree
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21 #end if
0
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22 #end if
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23 #if $export_result.export == "strain"
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24 strain
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25 #if $export_result.count
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26 -c
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27 #end if
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28 #end if
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29 #if $export_result.export == "gene"
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30 gene
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31 #end if
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32 #if str($mincover)
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33 -m $mincover
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34 #end if
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35 #if $keep
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36 -k
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37 #end if
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38 #if $inverse
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39 -V
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40 #end if
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41 #if $duplicate
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42 -d
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43 #end if
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44 '${database}'
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45 > '${$output}'
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46 #if $log
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47 2> '${logfile}'
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48 #end if
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49 </command>
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50 <inputs>
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51 <param name="database" type="data"
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52 format="sqlite"
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53 label="cg/wgMLST database"
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54 help="Sqlite format from cg/wgMLST database" />
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55 <conditional name="export_result">
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56 <param name="export" type="select" label="Select the data export">
1
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57 <option value="distance" selected="true">Distance matrix between strains on the cg/wgMLST database</option>
0
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58 <option value="mlst">cg/wgMLST table for each strain on the cg/wgMLST database</option>
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59 <option value="strain">List of the strains on the cg/wgMLST database</option>
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60 <option value="gene">List of the genes on the cg/wgMLST database</option>
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61 </param>
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62 <when value="strain">
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63 <param name="count" type="boolean" checked="false"
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64 label="Report the number of gene found for each strain" />
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65 </when>
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66 <when value="distance" />
1
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67 <when value="mlst">
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68 <param name="mlsttype" type="select"
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69 label="Select the format of export">
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70 <option value="default" selected="true">Default format</option>
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71 <option value="grapetree">Grapetree format</option>
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72 </param>
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73 </when>
0
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74 <when value="gene" />
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75 </conditional>
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76 <param name="mincover" type="integer" value="0"
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77 optional="true"
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78 label="Minimun number of strain found to keep a gene" />
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79 <param name="keep" type="boolean" checked="false"
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80 label="Keep only gene with different allele" help="Omit missing" />
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81 <param name="duplicate" type="boolean" checked="false"
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82 label="Conserve duplicate gene (default remove)" />
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83 <param name="inverse" type="boolean" checked="false"
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84 label="Keep only gene that not meet the filter of mincover or keep options" />
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85 <param name="log" type="boolean" checked="false"
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86 label="Write log file" />
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87 </inputs>
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88 <outputs>
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89 <data name="output" format="txt" label="Extract ${export_result.export} on ${database.name}">
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90 <change_format>
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91 <when input="export_result.export" value="mlst" format="tabular" />
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92 <when input="export_result.export" value="distance" format="txt" />
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93 <when input="export_result.export" value="strain" format="tabular" />
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94 <when input="export_result.export" value="gene" format="txt" />
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95 </change_format>
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96 </data>
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97 <data name="logfile" format="txt" label="${export_result.export} of ${database.name}: log">
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98 <filter>log</filter>
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99 </data>
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100 </outputs>
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101 <tests>
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102 <test expect_num_outputs="1">
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103 <param name="database" value="wgmlst_ecoli.db" />
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104 <conditional name="export_result">
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105 <param name="export" value="distance" />
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106 </conditional>
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107 <param name="mincover" value="4" />
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108 <output name="output" ftype="txt" file="wgmlst_ecoli.db.distance" />
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109 </test>
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110 <test expect_num_outputs="1">
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111 <param name="database" value="wgmlst_ecoli.db" />
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112 <conditional name="export_result">
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113 <param name="export" value="mlst" />
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114 </conditional>
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115 <param name="keep" value="true" />
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116 <output name="output" ftype="tabular" file="wgmlst_ecoli.db.mlst" />
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117 </test>
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118 <test expect_num_outputs="2">
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119 <param name="database" value="wgmlst_ecoli.db" />
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120 <conditional name="export_result">
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121 <param name="export" value="strain" />
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122 <param name="count" value="true" />
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123 </conditional>
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124 <param name="log" value="true" />
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125 <output name="output" ftype="tabular" file="wgmlst_ecoli.db.strain" />
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126 </test>
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127 <test expect_num_outputs="1">
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128 <param name="database" value="wgmlst_ecoli.db" />
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129 <conditional name="export_result">
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130 <param name="export" value="gene" />
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131 </conditional>
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132 <param name="keep" value="true" />
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133 <param name="inverse" value="true" />
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134 <output name="output" ftype="txt" file="wgmlst_ecoli.db.gene" />
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135 </test>
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136 </tests>
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137 <help>
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138 **What it does**
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139
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140 Extract element from a cg/wgMLST DATABASE:
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141 - an distance matrix
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142 - an MLST table
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143 - a gene list
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144 - an strains list
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145
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146 Options:
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147 -m, --mincover INTEGER Minimun number of strain found to keep a gene
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148 (default:0)
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149 -k, --keep Keep only gene with different allele (omit missing).
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150 -d, --duplicate Conserve duplicate gene (default remove).
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151 -V, --inverse Keep only gene that do not meet the filter of
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152 mincover or keep options.
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153
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154 -c, --count Count the number of gene present in the database for
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155 each strains.
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156
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157 **License and citation**
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158
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159 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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160 </help>
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161 <citations>
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162 </citations>
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163 </tool>