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20
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1 <tool id="xseeker_preparator" name="XSeeker Preparator" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
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19
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2 <description>prepares RData file from XCMS+CAMERA for XSeeker</description>
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20
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3 <macros>
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4 <token name="@VERSION@">1.3.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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2
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7 <edam_operations>
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8 <edam_operation>operation_1812</edam_operation>
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9 <edam_operation>operation_0335</edam_operation>
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10 </edam_operations>
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11 <requirements>
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20
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12 <requirement type="package" version="4.1.3">r-base</requirement>
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13 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
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15
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14 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
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14
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15 <requirement type="package" version="2.29.2">git</requirement>
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20
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16 <requirement type="package" version="1.2.3">r-blob</requirement>
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17 <requirement type="package" version="1.1.3">r-dbi</requirement>
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18 <requirement type="package" version="0.9.8">r-fst</requirement>
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4
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19 <requirement type="package" version="1.6.6">r-optparse</requirement>
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20 <requirement type="package" version="1.4.0">r-stringr</requirement>
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20
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21 <requirement type="package" version="0.3.5">r-purrr</requirement>
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22 <requirement type="package" version="2.2.18">r-rsqlite</requirement>
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14
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23 <requirement type="package" version="0.2.0">r-dbmodelr</requirement>
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2
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24 </requirements>
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25 <stdio>
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26 <exit_code
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27 range="1"
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28 level="warning"
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29 description="Selected samples have no data associated to them."
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30 />
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31 <exit_code
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32 range="2"
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33 level="warning"
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34 description="Some samples have no data associated to them."
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35 />
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36 </stdio>
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37 <version_command>
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4
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38 Rscript '$__tool_directory__/XSeekerPreparator.R' -v
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2
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39 </version_command>
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40 <command>
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41 <![CDATA[
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4
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42 Rscript '$__tool_directory__/XSeekerPreparator.R'
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2
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43 -P
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44 --input '$input'
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45 --output '$output'
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46 #if $samples.selected
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4
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47 --samples '${",".join($samples.selected)}'
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2
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48 #end if
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49 #if $database.archetypes
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50 --archetype '${",".join($database.archetypes)}'
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51 #end if
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52 #if $database.base.kind == "tabular"
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53 --compounds-csv '${database.base.tabular}'
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54 #else if $database.base.kind == "sql"
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55 --database '${database.base.sql}'
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56 #end if
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57 #if $database.models.kind == "default"
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58 --models '${base_config}'
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59 #else
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60 --models '${database.models.url}'
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61 #end if
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20
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62 #if $class
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63 --class '${class}'
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19
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64 #end if
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2
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65 ]]>
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66 </command>
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67 <configfiles>
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68 <configfile name="base_config">
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20
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69 <![CDATA[
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2
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70 tryCatch({
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71 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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72 }, error=function(e) {
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73 stop("Please, install DBModelR before you source this file.")
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74 })
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75 list(
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19
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76 adduct = DBModelR::ModelDefinition(
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77 table = "adduct",
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78 fields = list(
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79 name = "TEXT",
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80 mass = "FLOAT",
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81 charge = "INTEGER",
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82 multi = "INTEGER",
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83 formula_add = "TEXT",
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84 formula_ded = "TEXT",
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85 sign = "TEXT",
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86 oidscore = "INTEGER",
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87 quasi = "INTEGER",
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88 ips = "FLOAT"
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2
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89 )
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90 ),
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19
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91 cluster = DBModelR::ModelDefinition(
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92 table = "cluster",
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93 fields = list(
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94 clusterID = "INTEGER",
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95 formula = "TEXT",
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96 annotation = "TEXT",
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97 coeff = "FLOAT",
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98 r_squared = "FLOAT",
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99 charge = "INTEGER",
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100 mean_rt = "FLOAT",
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101 score = "FLOAT",
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102 deviation = "FLOAT",
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103 status = "TEXT",
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104 # adduct = "TEXT",
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105 curent_group = "INTEGER",
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106 pc_group = "INTEGER",
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107 align_group = "INTEGER",
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108 xcms_group = "INTEGER"
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2
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109 ),
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19
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110 one = list("compound", "adduct"),
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111 many = list("sample")
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2
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112 ),
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19
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113 compound = DBModelR::ModelDefinition(
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114 table = "compound",
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115 fields = list(
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116 name = "TEXT",
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117 common_name = "TEXT",
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118 formula = "TEXT",
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119 charge = "INTEGER",
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120 date = "TEXT",
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121 mz = "FLOAT"
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2
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122 )
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123 ),
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19
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124 feature = DBModelR::ModelDefinition(
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125 table = "feature",
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126 fields = list(
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127 featureID = "INTEGER",
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128 mz = "FLOAT",
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129 mz_min = "FLOAT",
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130 mz_max = "FLOAT",
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131 rt = "FLOAT",
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132 rt_min = "FLOAT",
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133 rt_max = "FLOAT",
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134 int_o = "FLOAT",
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135 int_b = "FLOAT",
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136 max_o = "FLOAT",
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137 iso = "TEXT",
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138 abundance = "FLOAT"
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2
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139 ),
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19
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140 one = list("cluster"),
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141 many = list("sample")
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2
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142 ),
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19
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143 instrument = DBModelR::ModelDefinition(
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144 table = "instrument",
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145 fields = list(
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146 model = "TEXT",
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147 manufacturer = "TEXT",
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148 analyzer = "TEXT",
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149 detector_type = "TEXT",
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150 ion_source = "TEXT"
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2
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151 )
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152 ),
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19
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153 instrument_config = DBModelR::ModelDefinition(
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154 table = "instrument_config",
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155 fields = list(
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156 resolution = "TEXT",
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157 agc_target = "TEXT",
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158 maximum_IT = "TEXT",
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159 number_of_scan_range = "TEXT",
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160 scan_range = "TEXT",
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161 version = "TEXT"
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2
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162 )
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163 ),
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19
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164 project = DBModelR::ModelDefinition(
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165 table = "project",
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166 fields = list(
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167 name = "TEXT",
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168 comment = "TEXT"
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2
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169 ),
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19
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170 one = list("sample")
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2
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171 ),
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19
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172 sample = DBModelR::ModelDefinition(
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173 table = "sample",
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174 fields = list(
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175 name = "TEXT",
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176 path = "TEXT",
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177 polarity = "TEXT",
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178 kind = "TEXT", ## rdata or mxml or enriched_rdata
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179 raw = "BLOB"
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2
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180 ),
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19
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181 one = list(
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2
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182 "peak_picking_parameters",
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183 "pairing_parameters",
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184 "alignmenmt_parameters",
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185 "camera_parameters",
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186 "instrument",
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187 "instrument_config",
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188 "software",
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189 "smol_xcms_set"
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190 )
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191 ),
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19
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192 smol_xcms_set = DBModelR::ModelDefinition(
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193 table = "smol_xcms_set",
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194 fields = list(
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195 raw = "BLOB"
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2
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196 )
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197 ),
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19
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198 software = DBModelR::ModelDefinition(
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199 table = "software",
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200 fields = list(
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201 name = "TEXT",
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202 version = "TEXT"
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2
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203 )
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204 ),
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19
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205 peak_picking_parameters = DBModelR::ModelDefinition(
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206 table = "peak_picking_parameters",
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207 fields = list(
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208 ppm = "FLOAT",
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209 peakwidth = "TEXT",
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210 snthresh = "TEXT",
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211 prefilterStep = "TEXT",
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212 prefilterLevel = "TEXT",
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213 mzdiff = "TEXT",
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214 fitgauss = "TEXT",
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215 noise = "TEXT",
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216 mzCenterFun = "TEXT",
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217 integrate = "INTEGER",
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218 firstBaselineCheck = "TEXT",
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219 snthreshIsoROIs = "TEXT",
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220 maxCharge = "INTEGER",
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221 maxIso = "INTEGER",
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222 mzIntervalExtension = "TEXT"
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2
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223 )
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224 ),
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19
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225 alignmenmt_parameters = DBModelR::ModelDefinition(
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226 table = "alignmenmt_parameters",
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227 fields = list(
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228 binSize = "TEXT",
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229 centerSample = "TEXT",
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230 response = "TEXT",
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231 distFun = "TEXT",
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232 gapInit = "TEXT",
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233 gapExtend = "TEXT",
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234 factorDiag = "TEXT",
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235 factorGap = "TEXT",
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236 localAlignment = "INTEGER",
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237 initPenalty = "TEXT",
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238 bw = "TEXT",
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239 minFraction = "TEXT",
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240 minSamples = "TEXT",
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241 maxFeatures = "TEXT"
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2
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242 )
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243 )
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244 )
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20
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245 ]]>
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2
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246 </configfile>
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247 </configfiles>
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20
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248 <inputs>
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249 <param
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250 argument="input"
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251 type="data"
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252 multiple="false"
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253 optional="false"
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254 format="rdata"
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255 label="Rdata to prepare"
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256 help="
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257 This rdata must be produced by a xcms+camera processing
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258 and original files must still be in the history.
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259 "
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260 >
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261 </param>
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262 <param
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263 argument="class"
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264 type="text"
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265 value=""
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266 label="Column class name"
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267 help="
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268 The name of the column containing the classes -
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269 leave empty to let XSeeker Preparator guess
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270 "
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271 optional="true"
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272 >
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273 </param>
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274 <section name="samples" title="Samples Options" expanded="false">
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275 <param
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276 name="selected"
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277 type="data"
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278 multiple="true"
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279 label="Samples to visualize"
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280 optional="true"
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281 format="mzml"
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282 >
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283 </param>
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284 </section>
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285 <section name="database" title="Database Options" expanded="false">
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286 <param
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287 name="archetypes"
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288 type="select"
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289 multiple="true"
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290 label="Molecule family (for database's compounds enrichment)"
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291 >
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292 <option value="G" selected="true">General</option>
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293 <option value="H">Halogenates</option>
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294 </param>
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295 <conditional name="base">
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296 <param name="kind" type="select" label="File containing compound's type">
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297 <option value="none" selected="true">None (default)</option>
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298 <option value="tabular">tabular</option>
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299 <option value="sql">sql</option>
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300 </param>
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301 <when value="none" />
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302 <when value="sql" />
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303 <when value="tabular">
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304 <param
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305 name="tabular"
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306 type="data"
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307 multiple="true"
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308 label="Tabular file containing compound to use in XSeeker"
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309 optional="true"
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310 format="tabular"
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311 >
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312 </param>
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313 </when>
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314 <when value="sql">
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315 <param
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316 name="sql"
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317 type="data"
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318 multiple="true"
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319 label="SQL file containing compound to use in XSeeker"
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320 optional="true"
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321 format="sql"
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322 >
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323 </param>
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324 </when>
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325 </conditional>
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326 <conditional name="models">
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327 <param name="kind" type="select" label="How is the database's model defined">
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328 <option value="default" selected="true">Default (regular XSeeker Database)</option>
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329 <option value="url">Download model file</option>
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330 <option value="git">Get versionned model file</option>
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331 </param>
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332 <when value="default" />
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333 <when value="url">
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334 <param name="url" type="text" format="url" label="File URL"/>
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335 </when>
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336 <when value="git">
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337 <param name="url" type="text" format="url" label="Repo URL"/>
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338 </when>
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339 </conditional>
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340 </section>
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341 </inputs>
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342 <outputs>
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343 <data format="sqlite" name="output" />
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344 <!-- <data format="xseeker.sqlite" name="output" /> -->
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345 </outputs>
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346 <help>
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347
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348 .. class:: infomark
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349
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350 **Authors** Lain Pavot (lain.pavot@inrae.fr)
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351
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352 --------------------------------------
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353
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354 ==================
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355 XSeeker Preparator
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356 ==================
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357
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358 -----------
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359 Description
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360 -----------
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361
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362 A preparation tool to precalculate and reorginize data from XCMS+CAMERA for
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363 XSeeker displayer tool to display them faster (from 30 min/some hours to some seconds).
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364
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365
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366 -----------------
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367 Workflow position
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368 -----------------
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369
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370 **Upstream tools**
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371
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372 ================ ======================== =========== ===============
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373 Name output file format parameter
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374 ================ ======================== =========== ===============
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375 CAMERA rdata.camera.quick rdata
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376 ================ ======================== =========== ===============
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377
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378
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379 **Downstream tools**
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380
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381 ================ ======================== =========== ===============
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382 Name output file format parameter
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383 ================ ======================== =========== ===============
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384 XSeeker sqlite sqlite3 NA
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385 ================ ======================== =========== ===============
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386
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387
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388
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389 -----------
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390 Input files
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391 -----------
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392
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393 Takes a rdata outputed by camera (after xcms) as input. The rdata has must have
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394 been produced using some mzml files - mxml files which must still be present
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395 in the history when doing xseekerpreparator:
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396 The rdata contains only some data and the paths to the original mzml files.
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397 These mzml files contains a lot of usefull informations needed to prepare
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398 the data for XSeeker. These files are not given as input, but are still
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399 needed.
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400
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401 ----------
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402 Parameters
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403 ----------
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404 Column class name:
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405 - the name of the column that defines classes in your sample metadata.
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406 Sample options:
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407 - provide mzml file names to process. Other files defined in the rdata will
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408 not be processed, and will not be available in xseeker.
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409 Database Options:
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410 - provide the molecular family you want to annotate, a compound file.
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411 - The database's model can be re-defined - only for devs users.
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412
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413 ------------
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414 Output files
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415 ------------
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416 An SQLite3 file is a database file that organizes data in such a way it is
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417 easily stored, filtered, modified, retrieved.
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418 </help>
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419 <citations></citations>
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2
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420 </tool>
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