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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ITRAQAnalyzer" name="ITRAQAnalyzer" version="2.0.0">
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3 <description>Calculates iTRAQ quantitative values for peptides</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ITRAQAnalyzer</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>ITRAQAnalyzer
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11
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12 #if $param_type:
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13 -type
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14 #if " " in str($param_type):
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15 "$param_type"
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16 #else
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17 $param_type
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18 #end if
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19 #end if
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20 #if $param_in:
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21 -in $param_in
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22 #end if
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23 #if $param_out:
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24 -out $param_out
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25 #end if
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26 #if $param_out_mzq:
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27 -out_mzq $param_out_mzq
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28 #end if
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29 #if $param_out_stats:
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30 -out_stats $param_out_stats
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31 #end if
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32 -threads \${GALAXY_SLOTS:-24}
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33 #if $param_id_pool:
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34 -id_pool "$param_id_pool"
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35 #end if
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36 #if $param_algorithm_Extraction_select_activation:
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37 -algorithm:Extraction:select_activation
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38 #if " " in str($param_algorithm_Extraction_select_activation):
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39 "$param_algorithm_Extraction_select_activation"
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40 #else
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41 $param_algorithm_Extraction_select_activation
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42 #end if
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43 #end if
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44 #if $param_algorithm_Extraction_reporter_mass_shift:
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45 -algorithm:Extraction:reporter_mass_shift $param_algorithm_Extraction_reporter_mass_shift
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46 #end if
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47
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48 #if $rep_param_algorithm_Extraction_channel_active:
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49 -algorithm:Extraction:channel_active
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50 #for token in $rep_param_algorithm_Extraction_channel_active:
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51 #if " " in str(token):
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52 "$token.param_algorithm_Extraction_channel_active"
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53 #else
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54 $token.param_algorithm_Extraction_channel_active
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55 #end if
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56 #end for
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57 #end if
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58 #if $param_algorithm_Quantification_channel_reference:
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59 -algorithm:Quantification:channel_reference $param_algorithm_Quantification_channel_reference
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60 #end if
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61 #if $adv_opts.adv_opts_selector=='advanced':
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62 #if $adv_opts.param_force:
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63 -force
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64 #end if
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65
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66 #if $rep_param_algorithm_Quantification_isotope_correction_4plex:
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67 -algorithm:Quantification:isotope_correction:4plex
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68 #for token in $rep_param_algorithm_Quantification_isotope_correction_4plex:
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69 #if " " in str(token):
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70 "$token.param_algorithm_Quantification_isotope_correction_4plex"
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71 #else
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72 $token.param_algorithm_Quantification_isotope_correction_4plex
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73 #end if
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74 #end for
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75 #end if
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76
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77 #if $rep_param_algorithm_Quantification_isotope_correction_8plex:
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78 -algorithm:Quantification:isotope_correction:8plex
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79 #for token in $rep_param_algorithm_Quantification_isotope_correction_8plex:
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80 #if " " in str(token):
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81 "$token.param_algorithm_Quantification_isotope_correction_8plex"
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82 #else
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83 $token.param_algorithm_Quantification_isotope_correction_8plex
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84 #end if
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85 #end for
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86 #end if
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87 #if $adv_opts.param_algorithm_Quantification_do_normalization:
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88 -algorithm:Quantification:do_normalization
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89 #end if
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90 #if $adv_opts.param_algorithm_MetaInformation_Program:
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91 -algorithm:MetaInformation:Program "$adv_opts.param_algorithm_MetaInformation_Program"
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92 #end if
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93 #end if
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94 </command>
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95 <inputs>
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96 <param name="param_type" type="select" optional="True" value="4plex" label="iTRAQ experiment type" help="(-type) ">
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97 <option value="4plex">4plex</option>
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98 <option value="8plex">8plex</option>
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99 </param>
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100 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
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101 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/thouwaar/Downloads/openms-2.0-Linux-x86_64/share/OpenMS/IDPool/IDPool.txt)">
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102 <sanitizer>
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103 <valid initial="string.printable">
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104 <remove value="'"/>
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105 <remove value="""/>
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106 </valid>
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107 </sanitizer>
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108 </param>
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109 <param name="param_algorithm_Extraction_select_activation" type="select" optional="True" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ)" help="(-select_activation) Set to empty string if you want to disable filtering">
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110 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
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111 <option value="Post-source decay">Post-source decay</option>
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112 <option value="Plasma desorption">Plasma desorption</option>
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113 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
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114 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
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115 <option value="Electron capture dissociation">Electron capture dissociation</option>
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116 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
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117 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
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118 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
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119 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
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120 <option value="Photodissociation">Photodissociation</option>
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121 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
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122 <option value=""></option>
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123 </param>
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124 <param name="param_algorithm_Extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/>
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125 <repeat name="rep_param_algorithm_Extraction_channel_active" min="0" max="1" title="param_algorithm_Extraction_channel_active">
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126 <param name="param_algorithm_Extraction_channel_active" type="text" size="30" value="114:liver 117:lung" label="Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex) in format <channel>:<name>," help="(-channel_active) e.g. "114:myref","115:liver"">
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127 <sanitizer>
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128 <valid initial="string.printable">
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129 <remove value="'"/>
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130 <remove value="""/>
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131 </valid>
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132 </sanitizer>
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133 </param>
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134 </repeat>
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135 <param name="param_algorithm_Quantification_channel_reference" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117 for 4plex)" help="(-channel_reference) "/>
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136 <expand macro="advanced_options">
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137 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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138 <repeat name="rep_param_algorithm_Quantification_isotope_correction_4plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_4plex">
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139 <param name="param_algorithm_Quantification_isotope_correction_4plex" type="text" size="30" value="114:0/1/5.9/0.2 115:0/2/5.6/0.1 116:0/3/4.5/0.1 117:0.1/4/3.5/0.1" label="Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" help="(-4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'">
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140 <sanitizer>
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141 <valid initial="string.printable">
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142 <remove value="'"/>
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143 <remove value="""/>
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144 </valid>
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145 </sanitizer>
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146 </param>
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147 </repeat>
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148 <repeat name="rep_param_algorithm_Quantification_isotope_correction_8plex" min="0" max="1" title="param_algorithm_Quantification_isotope_correction_8plex">
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149 <param name="param_algorithm_Quantification_isotope_correction_8plex" type="text" size="30" value="113:0/0/6.89/0.22 114:0/0.94/5.9/0.16 115:0/1.88/4.9/0.1 116:0/2.82/3.9/0.07 117:0.06/3.77/2.99/0 118:0.09/4.71/1.88/0 119:0.14/5.66/0.87/0 121:0.27/7.44/0.18/0" label="Override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ;" help="(-8plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'">
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150 <sanitizer>
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151 <valid initial="string.printable">
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152 <remove value="'"/>
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153 <remove value="""/>
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154 </valid>
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155 </sanitizer>
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156 </param>
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157 </repeat>
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158 <param name="param_algorithm_Quantification_do_normalization" type="boolean" truevalue="-algorithm:Quantification:do_normalization" falsevalue="" checked="false" optional="True" label="Normalize channels?" help="(-do_normalization) Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/>
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159 <param name="param_algorithm_MetaInformation_Program" type="text" size="30" value="OpenMS::ITRAQAnalyzer" label="" help="(-Program) ">
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160 <sanitizer>
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161 <valid initial="string.printable">
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162 <remove value="'"/>
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163 <remove value="""/>
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164 </valid>
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165 </sanitizer>
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166 </param>
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167 </expand>
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168 </inputs>
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169 <outputs>
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170 <data name="param_out" format="consensusxml"/>
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171 <data name="param_out_mzq" format="mzq"/>
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172 <data name="param_out_stats" format="tabular"/>
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173 </outputs>
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174 <help>**What it does**
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175
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176 Calculates iTRAQ quantitative values for peptides
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177
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178
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179 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ITRAQAnalyzer.html</help>
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180 <expand macro="references"/>
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181 </tool>
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