Mercurial > repos > recetox > ramclustr_define_experiment

annotate ramclustr_define_experiment.xml @ 1:2e012f4c062e draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8714723083359049eb1a715a946851e07f8a3a20
author recetox
date Tue, 20 Sep 2022 14:44:32 +0000
parents 42c2a25ff197
children 25625114618e
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1 <tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2">
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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="creator"/>
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7
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8 <command detect_errors="exit_code"><![CDATA[
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9 sh ${ramclustr_define_experiment_cli}
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10 ]]>
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11 </command>
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12 <configfiles>
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13 <configfile name="ramclustr_define_experiment_cli">
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14 python3 ${__tool_directory__}/ramclustr_define_experiment_wrapper.py \
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15 --Experiment "$design.Experiment" \
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16 --Species "$design.Species" \
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17 --Sample "$design.Sample" \
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18 --Contributer "$design.Contributor" \
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19 --platform "$platform.platform_choice.choice" \
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20 #if $platform.platform_choice.choice == "GC-MS":
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21 --chrominst "$platform.platform_choice.chrominst" \
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22 --msinst "$platform.platform_choice.msinst" \
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23 --column "$platform.platform_choice.column" \
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24 --InletTemp "$platform.platform_choice.InletTemp" \
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25 --TransferTemp "$platform.platform_choice.TransferTemp" \
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26 --mstype "$platform.platform_choice.gc_mstype" \
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27 --msmode "$platform.platform_choice.msmode" \
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28 --ionization "$platform.platform_choice.gc_ionization" \
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29 --msscanrange "$platform.platform_choice.msscanrange" \
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30 --scantime "$platform.platform_choice.scantime" \
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31 --deriv "$platform.platform_choice.deriv" \
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32 --MSlevs "$platform.platform_choice.MSlevs" \
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33 #else:
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34 --chrominst "$platform.platform_choice.chrominst" \
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35 --msinst "$platform.platform_choice.msinst" \
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36 --column "$platform.platform_choice.column" \
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37 --solvA "$platform.platform_choice.solvA" \
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38 --solvB "$platform.platform_choice.solvB" \
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39 --CE1 "$platform.platform_choice.CE1" \
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40 --CE2 "$platform.platform_choice.CE2" \
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41 --mstype "$platform.platform_choice.lc_mstype" \
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42 --msmode "$platform.platform_choice.msmode" \
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43 --ionization "$platform.platform_choice.lc_ionization" \
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44 --colgas "$platform.platform_choice.colgas" \
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45 --msscanrange "$platform.platform_choice.msscanrange" \
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46 --conevol "$platform.platform_choice.conevol" \
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47 --MSlevs "$platform.platform_choice.MSlevs" \
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48 #end if
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49 --output_file "$RAMClustR_experiment"
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50 </configfile>
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51 </configfiles>
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52 <inputs>
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53 <section name="design" title="Experimental Design" expanded="true">
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54 <param name="Experiment" type="text" label="Experiment name (no spaces).">
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55 <validator type="empty_field"/>
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56 </param>
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57 <param name="Species" type="text" label="Genus species from which samples are derived."/>
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58 <param name="Sample" type="text" label="Type of sample (e.g., serum, leaf)."/>
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59 <param name="Contributor" type="text" label="Your or your PI's name."/>
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60 </section>
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61
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62 <section name="platform" title="Platform" expanded="true">
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63 <conditional name="platform_choice">
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64 <param name="choice" type="select" label="Choose platform:">
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65 <option value="GC-MS" selected="true">GC-MS</option>
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66 <option value="LC-MS">LC-MS</option>
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67 </param>
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68 <when value="GC-MS">
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69 <param name="chrominst" type="text" label="Model of GC instrument."/>
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70 <param name="msinst" type="text" label="Model of MS instrument."/>
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71 <param name="column" type="text" label="Column description."/>
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72 <param name="InletTemp" type="text" label="Temperature of inlet."/>
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73 <param name="TransferTemp" type="text" label="Temperature of GC to MS transfer line."/>
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74 <param name="gc_mstype" type="select" label="Type of mass spectrometer:">
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75 <option value="QQQ" selected="true">QQQ</option>
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76 <option value="TOF">TOF</option>
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77 <option value="QTOF">QTOF</option>
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78 <option value="Orbi">Orbi</option>
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79 <option value="Q">Q</option>
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80 </param>
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81 <param name="msmode" type="select" label="Ion mode:">
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82 <option value="positive" selected="true">positive</option>
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83 <option value="negative">negative</option>
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84 </param>
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85 <param name="gc_ionization" type="select" label="Ionization:">
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86 <option value="EI" selected="true">EI</option>
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87 <option value="AP">AP</option>
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88 <option value="CI">CI</option>
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89 </param>
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90 <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
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91 <param name="scantime" type="float" value="0.2" label="Time for each full scan spectrum (e.g. 0.2 seconds)."/>
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92 <param name="deriv" type="select" label="Derivitization:">
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93 <option value="TMS" selected="true">TMS</option>
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94 <option value="TBDMS">TBDMS</option>
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95 <option value="None">None</option>
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96 </param>
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97 <param name="MSlevs" type="float" value="1" label="Number of levels of energy acquired - 1 typically."/>
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98 </when>
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99 <when value="LC-MS">
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100 <param name="chrominst" type="text" label="Model of LC instrument."/>
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101 <param name="msinst" type="text" label="Model of MS instrument."/>
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102 <param name="column" type="text" label="Column description."/>
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103 <param name="solvA" type="text" label="Solvent A composition."/>
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104 <param name="solvB" type="text" label="Solvent B composition."/>
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105 <param name="CE1" type="text" label="Collision energy of acquisition of MS data."/>
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106 <param name="CE2" type="text" label="Collision energy of acquisition for MSe/idMSMS data (when applicable)."/>
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107 <param name="lc_mstype" type="select" label="Type of mass spectrometer:">
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108 <option value="QQQ" selected="true">QQQ</option>
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109 <option value="TOF">TOF</option>
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110 <option value="QTOF">QTOF</option>
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111 <option value="Orbi">Orbi</option>
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112 <option value="Q">Q</option>
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113 </param>
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114 <param name="msmode" type="select" label="Ion mode:">
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115 <option value="positive" selected="true">positive</option>
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116 <option value="negative">negative</option>
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117 </param>
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118 <param name="lc_ionization" type="select" label="Ionization:">
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119 <option value="ESI" selected="true">ESI</option>
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120 <option value="APCI">APCI</option>
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121 </param>
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122 <param name="colgas" type="text" label="Gas used for collisional dissociation."/>
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123 <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
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124 <param name="conevol" type="text" label="Cone voltage used for acquisition."/>
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125 <param name="MSlevs" type="float" value="1" label="number of levels of energy in XCMS object data - 1 typically."/>
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126 </when>
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127 </conditional>
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128 </section>
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129 </inputs>
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130
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131 <outputs>
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132 <data label="RAMClustR experiment definition" name="RAMClustR_experiment" format="csv" />
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133 </outputs>
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134
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135 <tests>
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136 <test><!-- TEST 1 -->
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137 <section name="design">
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138 <param name="Experiment" value="experiment_gc"/>
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139 <param name="Species" value="mus musculus"/>
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140 <param name="Sample" value="serum"/>
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141 <param name="Contributor" value="recetox"/>
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142 </section>
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143 <section name="platform">
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144 <section name="platform_choice">
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145 <param name="choice" value="GC-MS"/>
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146 <param name="chrominst" value="ISQ 7000"/>
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147 <param name="msinst" value="ISQ7K-VPI"/>
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148 <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
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149 <param name="InletTemp" value="33"/>
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150 <param name="TransferTemp" value="23"/>
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151 <param name="gc_mstype" value="QTOF"/>
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152 <param name="msmode" value="positive"/>
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153 <param name="gc_ionization" value="AP"/>
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154 <param name="msscanrange" value="100"/>
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155 <param name="scantime" value="0.2"/>
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156 <param name="deriv" value="TMS"/>
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157 <param name="MSlevs" value="1.0"/>
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158 </section>
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159 </section>
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160 <output name="RAMClustR_experiment" file="gc-ramclustr-define-experiment.csv" ftype="csv"/>
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161 </test>
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162 <test><!-- TEST 2 -->
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163 <section name="design">
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164 <param name="Experiment" value="experiment_lc"/>
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165 <param name="Species" value="mus musculus"/>
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166 <param name="Sample" value="serum"/>
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167 <param name="Contributor" value="recetox"/>
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168 </section>
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169 <section name="platform">
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170 <section name="platform_choice">
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171 <param name="choice" value="LC-MS"/>
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172 <param name="chrominst" value="UltiMateX 3000 BioRS System"/>
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173 <param name="msinst" value="FSN04-10000"/>
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174 <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
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175 <param name="solvA" value="H20"/>
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176 <param name="solvB" value="CO2"/>
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177 <param name="CE1" value="50"/>
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178 <param name="CE2" value="100"/>
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179 <param name="lc_mstype" value="Q"/>
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180 <param name="msmode" value="negative"/>
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181 <param name="lc_ionization" value="ESI"/>
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182 <param name="colgas" value="He"/>
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183 <param name="msscanrange" value="1000"/>
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184 <param name="conevol" value="12"/>
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185 <param name="MSlevs" value="1.0"/>
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186 </section>
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187 </section>
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188 <output name="RAMClustR_experiment" file="lc-ramclustr-define-experiment.csv" ftype="csv"/>
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189 </test>
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190 </tests>
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191
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192 <help>
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193 <![CDATA[
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194 @HELP_experiment@
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195 ]]>
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196 </help>
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197
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198 <expand macro="citations" />
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199 </tool>