Mercurial > repos > recetox > ramclustr_define_experiment

annotate ramclustr_define_experiment.xml @ 7:7c50666b88e8 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e
author recetox
date Wed, 17 Apr 2024 07:51:35 +0000
parents 7bbdcce50541
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1 <tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2+galaxy2" profile="21.09">
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2 <description>Definition of experimental design used for record keeping and writing spectra data.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro='annotation'/>
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7 <edam_operations>
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8 <edam_operation>operation_3429</edam_operation>
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9 </edam_operations>
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10 <expand macro="refs"/>
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11 <expand macro="creator"/>
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12
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13 <command detect_errors="exit_code"><![CDATA[
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14 sh ${ramclustr_define_experiment_cli}
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15 ]]>
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16 </command>
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17 <configfiles>
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18 <configfile name="ramclustr_define_experiment_cli">
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19 python3 ${__tool_directory__}/ramclustr_define_experiment_wrapper.py \
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20 --Experiment "$design.Experiment" \
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21 --Species "$design.Species" \
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22 --Sample "$design.Sample" \
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23 --Contributer "$design.Contributor" \
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24 --platform "$platform.platform_choice.choice" \
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25 #if $platform.platform_choice.choice == "GC-MS":
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26 --chrominst "$platform.platform_choice.chrominst" \
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27 --msinst "$platform.platform_choice.msinst" \
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28 --column "$platform.platform_choice.column" \
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29 --InletTemp "$platform.platform_choice.InletTemp" \
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30 --TransferTemp "$platform.platform_choice.TransferTemp" \
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31 --mstype "$platform.platform_choice.gc_mstype" \
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32 --msmode "$platform.platform_choice.msmode" \
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33 --ionization "$platform.platform_choice.gc_ionization" \
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34 --msscanrange "$platform.platform_choice.msscanrange" \
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35 --scantime "$platform.platform_choice.scantime" \
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36 --deriv "$platform.platform_choice.deriv" \
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37 --MSlevs "$platform.platform_choice.MSlevs" \
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38 #else:
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39 --chrominst "$platform.platform_choice.chrominst" \
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40 --msinst "$platform.platform_choice.msinst" \
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41 --column "$platform.platform_choice.column" \
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42 --solvA "$platform.platform_choice.solvA" \
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43 --solvB "$platform.platform_choice.solvB" \
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44 --CE1 "$platform.platform_choice.CE1" \
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45 --CE2 "$platform.platform_choice.CE2" \
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46 --mstype "$platform.platform_choice.lc_mstype" \
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47 --msmode "$platform.platform_choice.msmode" \
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48 --ionization "$platform.platform_choice.lc_ionization" \
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49 --colgas "$platform.platform_choice.colgas" \
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50 --msscanrange "$platform.platform_choice.msscanrange" \
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51 --conevol "$platform.platform_choice.conevol" \
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52 --MSlevs "$platform.platform_choice.MSlevs" \
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53 #end if
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54 --output_file "$RAMClustR_experiment"
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55 </configfile>
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56 </configfiles>
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57 <inputs>
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58 <section name="design" title="Experimental Design" expanded="true">
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59 <param name="Experiment" type="text" label="Experiment name (no spaces).">
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60 <validator type="empty_field"/>
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61 </param>
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62 <param name="Species" type="text" label="Genus species from which samples are derived."/>
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63 <param name="Sample" type="text" label="Type of sample (e.g., serum, leaf)."/>
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64 <param name="Contributor" type="text" label="Your or your PI's name."/>
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65 </section>
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66
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67 <section name="platform" title="Platform" expanded="true">
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68 <conditional name="platform_choice">
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69 <param name="choice" type="select" label="Choose platform:">
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70 <option value="GC-MS" selected="true">GC-MS</option>
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71 <option value="LC-MS">LC-MS</option>
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72 </param>
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73 <when value="GC-MS">
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74 <param name="chrominst" type="text" label="Model of GC instrument."/>
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75 <param name="msinst" type="text" label="Model of MS instrument."/>
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76 <param name="column" type="text" label="Column description."/>
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77 <param name="InletTemp" type="text" label="Temperature of inlet."/>
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78 <param name="TransferTemp" type="text" label="Temperature of GC to MS transfer line."/>
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79 <param name="gc_mstype" type="select" label="Type of mass spectrometer:">
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80 <option value="QQQ" selected="true">QQQ</option>
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81 <option value="TOF">TOF</option>
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82 <option value="QTOF">QTOF</option>
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83 <option value="Orbi">Orbi</option>
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84 <option value="Q">Q</option>
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85 </param>
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86 <param name="msmode" type="select" label="Ion mode:">
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87 <option value="positive" selected="true">positive</option>
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88 <option value="negative">negative</option>
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89 </param>
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90 <param name="gc_ionization" type="select" label="Ionization:">
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91 <option value="EI" selected="true">EI</option>
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92 <option value="AP">AP</option>
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93 <option value="CI">CI</option>
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94 </param>
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95 <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
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96 <param name="scantime" type="float" value="0.2" label="Time for each full scan spectrum (e.g. 0.2 seconds)."/>
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97 <param name="deriv" type="select" label="Derivitization:">
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98 <option value="TMS" selected="true">TMS</option>
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99 <option value="TBDMS">TBDMS</option>
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100 <option value="None">None</option>
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101 </param>
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102 <param name="MSlevs" type="float" value="1" label="Number of levels of energy acquired - 1 typically."/>
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103 </when>
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104 <when value="LC-MS">
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105 <param name="chrominst" type="text" label="Model of LC instrument."/>
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106 <param name="msinst" type="text" label="Model of MS instrument."/>
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107 <param name="column" type="text" label="Column description."/>
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108 <param name="solvA" type="text" label="Solvent A composition."/>
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109 <param name="solvB" type="text" label="Solvent B composition."/>
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110 <param name="CE1" type="text" label="Collision energy of acquisition of MS data."/>
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111 <param name="CE2" type="text" label="Collision energy of acquisition for MSe/idMSMS data (when applicable)."/>
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112 <param name="lc_mstype" type="select" label="Type of mass spectrometer:">
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113 <option value="QQQ" selected="true">QQQ</option>
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114 <option value="TOF">TOF</option>
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115 <option value="QTOF">QTOF</option>
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116 <option value="Orbi">Orbi</option>
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117 <option value="Q">Q</option>
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118 </param>
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119 <param name="msmode" type="select" label="Ion mode:">
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120 <option value="positive" selected="true">positive</option>
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121 <option value="negative">negative</option>
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122 </param>
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123 <param name="lc_ionization" type="select" label="Ionization:">
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124 <option value="ESI" selected="true">ESI</option>
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125 <option value="APCI">APCI</option>
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126 </param>
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127 <param name="colgas" type="text" label="Gas used for collisional dissociation."/>
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128 <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
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129 <param name="conevol" type="text" label="Cone voltage used for acquisition."/>
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130 <param name="MSlevs" type="float" value="1" label="number of levels of energy in XCMS object data - 1 typically."/>
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131 </when>
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132 </conditional>
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133 </section>
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134 </inputs>
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135
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136 <outputs>
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137 <data label="RAMClustR experiment definition" name="RAMClustR_experiment" format="csv" />
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138 </outputs>
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139
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140 <tests>
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141 <test><!-- TEST 1 -->
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142 <section name="design">
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143 <param name="Experiment" value="experiment_gc"/>
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144 <param name="Species" value="mus musculus"/>
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145 <param name="Sample" value="serum"/>
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146 <param name="Contributor" value="recetox"/>
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147 </section>
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148 <section name="platform">
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149 <section name="platform_choice">
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150 <param name="choice" value="GC-MS"/>
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151 <param name="chrominst" value="ISQ 7000"/>
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152 <param name="msinst" value="ISQ7K-VPI"/>
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153 <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
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154 <param name="InletTemp" value="33"/>
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155 <param name="TransferTemp" value="23"/>
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156 <param name="gc_mstype" value="QTOF"/>
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157 <param name="msmode" value="positive"/>
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158 <param name="gc_ionization" value="AP"/>
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159 <param name="msscanrange" value="100"/>
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160 <param name="scantime" value="0.2"/>
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161 <param name="deriv" value="TMS"/>
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162 <param name="MSlevs" value="1.0"/>
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163 </section>
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164 </section>
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165 <output name="RAMClustR_experiment" file="gc-ramclustr-define-experiment.csv" ftype="csv"/>
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166 </test>
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167 <test><!-- TEST 2 -->
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168 <section name="design">
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169 <param name="Experiment" value="experiment_lc"/>
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170 <param name="Species" value="mus musculus"/>
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171 <param name="Sample" value="serum"/>
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172 <param name="Contributor" value="recetox"/>
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173 </section>
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174 <section name="platform">
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175 <section name="platform_choice">
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176 <param name="choice" value="LC-MS"/>
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177 <param name="chrominst" value="UltiMateX 3000 BioRS System"/>
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178 <param name="msinst" value="FSN04-10000"/>
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179 <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
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180 <param name="solvA" value="H20"/>
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181 <param name="solvB" value="CO2"/>
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182 <param name="CE1" value="50"/>
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183 <param name="CE2" value="100"/>
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184 <param name="lc_mstype" value="Q"/>
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185 <param name="msmode" value="negative"/>
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186 <param name="lc_ionization" value="ESI"/>
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187 <param name="colgas" value="He"/>
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188 <param name="msscanrange" value="1000"/>
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189 <param name="conevol" value="12"/>
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190 <param name="MSlevs" value="1.0"/>
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191 </section>
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192 </section>
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193 <output name="RAMClustR_experiment" file="lc-ramclustr-define-experiment.csv" ftype="csv"/>
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194 </test>
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195 </tests>
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196
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197 <help>
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198 <![CDATA[
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199 @HELP_experiment@
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200 ]]>
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201 </help>
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202
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203 <expand macro="citations" />
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204 </tool>