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1 <tool id="msconvert3" name="msconvert3" version="0.2.0">
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2 <!-- BEGIN_VERSION_DEFAULT -->
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3 <description>Convert and filter a mass spec peak list</description>
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4 <!-- END_VERSION_DEFAULT -->
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5
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6 <command interpreter="python">
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3
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7 #set $ext = $input.ext
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8 #if $ext.startswith("m:")
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9 #set $ext = $ext[len("m:"):]
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10 #end if
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11 msconvert_wrapper.py
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12 --input=${input}
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13 #if hasattr($input, 'display_name')
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14 --input_name='${input.display_name}'
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15 #end if
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16 --output=${output}
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17 ## BEGIN_VERSION_DEFAULT
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18 --fromextension=$ext
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19 ## END_VERSION_DEFAULT
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20
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21
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22 --toextension=${output_type}
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23
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24 #if $settings.settingsType == "full"
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25 --binaryencoding=${settings.binary_encoding}
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26 --mzencoding=${settings.mz_encoding}
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27 --intensityencoding=${settings.intensity_encoding}
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28 --zlib=${settings.zlib}
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29 #end if
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30
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31 #if $filtering.filtering_use
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32
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33 #if $filtering.precursor_recalculation.value
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34 --filter "precursorRecalculation"
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35 #end if
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36
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37 #if $filtering.peak_picking.pick_peaks
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38 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
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39 #end if
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40
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41 #if str($filtering.activation) != "false"
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42 --filter "activation $filtering.activation"
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43 #end if
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44
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45 #if len($filtering.indices) > 0
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46 --filter "index
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47 #for $index in $filtering.indices
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48 [${index.from},${index.to}]
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49 #end for
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50 "
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51 #end if
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52
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53 #if len($filtering.scan_numbers) > 0
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54 --filter "scanNumber
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55 #for $scan_number in $filtering.scan_numbers
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56 [${scan_number.from},${scan_number.to}]
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57 #end for
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58 "
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59 #end if
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60
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61 #for threshold_entry in $filtering.threshold_repeat
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62 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
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63 #end for
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64
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65
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66 #if $filtering.strip_it.value
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67 --filter "stripIT"
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68 #end if
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69
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70 #if $filtering.filter_mz_windows.do_filter
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71 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
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72 #end if
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73
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74
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75 #if $filtering.filter_ms_levels.do_filter
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76 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
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77 #end if
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78
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79 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
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80 --filter "ETDFilter"
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81 #end if
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82
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83 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
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84 --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
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85 #end if
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86
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87 ## BEGIN_VERSION_3
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88
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89 #if $filtering.precursor_refine.value
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90 --filter "precursorRefine"
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91 #end if
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92
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93 #if $filtering.ms2denoise.denoise
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94 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
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95 #end if
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96
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97 #if str($filtering.ms2deisotope) == "true"
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98 --filter "MS2Deisotope"
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99 #end if
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100
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101 #if str($filtering.polarity) != "false"
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102 --filter "polarity $filtering.polarity"
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103 #end if
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104
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105 #if str($filtering.analyzer) != "false"
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106 --filter "analyzer $filtering.analyzer"
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107 #end if
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108
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109 ## END_VERSION_3
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110
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111 #end if
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112
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113 </command>
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114
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115 <inputs>
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116
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117 <!-- BEGIN_VERSION_DEFAULT -->
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118 <conditional name="type">
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119 <param name="input_type" type="select" label="Input Type">
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120 <option value="mzml">mzML</option>
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121 <option value="mzxml">mzXML</option>
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122 <option value="mgf">mgf</option>
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123 <option value="ms2">ms2</option>
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124 </param>
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125 <when value="mzml">
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126 <param format="mzml" name="input" type="data" label="Input mzML"/>
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127 </when>
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128 <when value="mzxml">
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129 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
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130 </when>
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131 <when value="mgf">
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132 <param format="mgf" name="input" type="data" label="Input mgf"/>
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133 </when>
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134 <when value="ms2">
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135 <param format="ms2" name="input" type="data" label="Input ms2"/>
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136 </when>
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137 </conditional>
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138 <!-- END_VERSION_DEFAULT -->
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139 <param name="output_type" type="select" label="Output Type">
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140 <option value="mzML">mzML (indexed)</option>
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141 <option value="unindexed_mzML">mzML (unindexed)</option>
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142 <option value="mzXML">mzXML (indexed)</option>
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143 <option value="unindexed_mzXML">mzXML (unindexed)</option>
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144 <option value="mgf">mgf</option>
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145 <option value="ms2">ms2</option>
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146 </param>
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147 <conditional name="filtering">
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148 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
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149 <when value="false" />
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150 <when value="true">
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151 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
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152 <!-- BEGIN_VERSION_3 -->
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153 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
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154 <!-- END_VERSION_3 -->
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155
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156
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157 <conditional name="peak_picking">
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158 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
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159 <when value="false" />
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160 <when value="true">
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161 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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162 <option value="1">MS1 Only (1)</option>
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163 <option value="2">MS2 Only (2)</option>
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164 <option value="2-">MS2 and on (2-)</option>
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165 <option value="1-">All Levels (1-)</option>
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166 </param>
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167 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
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168 </when>
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169 </conditional>
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170
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171 <repeat name="threshold_repeat" title="Filter by Threshold">
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172 <conditional name="threshold">
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173 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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174 <option value="count">Peak count</option>
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175 <option value="count-after-ties">Peak count (after ties)</option>
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176 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
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177 <option value="bpi-relative">Percent of base peak intensity</option>
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178 <option value="tic-relative">Percent of total ion current</option>
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179 <option value="tic-fraction">Aggregate percent of total ion current</option>
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180 </param>
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181 <when value="count">
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182 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
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183 </when>
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184 <when value="count-after-ties">
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185 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
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186 </when>
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187 <when value="absolute">
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188 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
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189 </when>
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190 <when value="bpi-relative">
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191 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
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192 />
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193 </when>
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194 <when value="tic-relative">
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195 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
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196 />
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197 </when>
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198 <when value="tic-fraction">
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199 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
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200 </when>
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201 </conditional>
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202 <param type="select" label="Keep" name="orientation">
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203 <option value="most-intense">Most intense peaks</option>
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204 <option value="least-intense">Least intense peaks</option>
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205 </param>
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206 </repeat>
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207
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208
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209 <param name="activation" type="select" label="Filter by Activation">
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210 <option value="false" selected="true">no</option>
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211 <option value="ETD">ETD</option>
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212 <option value="CID">CID</option>
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213 <option value="SA">SA</option>
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214 <option value="HCD">HCD</option>
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215 <!-- BEGIN_VERSION_3 -->
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216 <option>BIRD</option>
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217 <option>ECD</option>
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218 <option>IRMPD</option>
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219 <option>PD</option>
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220 <option>PSD</option>
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221 <option>PQD</option>
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222 <option>SID</option>
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223 <option>SORI</option>
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224 <!-- END_VERSION_3 -->
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225 </param>
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226
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227 <repeat name="indices" title="Filter Scan Indices">
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228 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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229 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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230 </repeat>
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231
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232 <repeat name="scan_numbers" title="Filter Scan Numbers">
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233 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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234 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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235 </repeat>
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236
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237 <conditional name="filter_mz_windows">
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238 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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239 <when value="false" />
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240 <when value="true">
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241 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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242 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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243 </when>
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244 </conditional>
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245
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246 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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247
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248 <conditional name="filter_ms_levels">
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249 <param name="do_filter" type="boolean" label="Filter MS Levels" />
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250 <when value="false" />
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251 <when value="true">
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252 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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253 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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254 </when>
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255 </conditional>
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256
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257 <conditional name="etd_filtering">
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258 <param name="do_etd_filtering" type="select" label="ETD Filtering">
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259 <option value="none" selected="true">none</option>
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260 <option value="default">yes (with default options)</option>
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261 <option value="advanced">yes (show advanced options) </option>
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262 </param>
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263 <when value="none" />
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264 <when value="default" />
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265 <when value="advanced">
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266 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
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267 </param>
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268 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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269 <option value="MZ" selected="true">mz</option>
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270 <option value="PPM">ppm</option>
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271 </param>
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272 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
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273 <option value="true" selected="true">yes</option>
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274 <option value="false">no</option>
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275 </param>
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276 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
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277 <option value="true" selected="true">yes</option>
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278 <option value="false">no</option>
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279 </param>
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280 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
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281 <option value="true" selected="true">yes</option>
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282 <option value="false">no</option>
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283 </param>
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284 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
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285 <option value="true" selected="true">yes</option>
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286 <option value="false">no</option>
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287 </param>
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288 </when>
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289 </conditional>
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290
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291
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292 <!-- BEGIN_VERSION_3 -->
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293 <conditional name="ms2denoise">
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294 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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295 <when value="true">
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296 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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297 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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298 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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299 </when>
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300 <when value="false" />
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301 </conditional>
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302 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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303
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304 <param name="polarity" type="select" label="Filter by Polarity">
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305 <option value="false" selected="true">no</option>
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306 <option value="positive">positive</option>
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307 <option value="negative">negative</option>
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308 </param>
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309
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310 <param name="analyzer" type="select" label="Filter by Analyzer">
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311 <option value="false" selected="true">no</option>
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312 <option value="quad">quad</option>
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313 <option value="orbi">orbi</option>
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314 <option value="FT">FT</option>
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315 <option value="IT">IT</option>
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316 <option value="TOF">TOF</option>
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317 </param>
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318 <!-- END_VERSION_3 -->
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319 </when>
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320 </conditional>
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321
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322 <conditional name="settings">
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323 <param name="settingsType" type="select" label="Advanced Settings" help="">
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324 <option value="default">Use Defaults</option>
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325 <option value="full">Full Parameter List</option>
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326 </param>
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327 <when value="default" />
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328 <when value="full">
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329 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
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330 <option value="64" selected="true">64</option>
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331 <option value="32">32</option>
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332 </param>
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333 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
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334 <option value="64" selected="true">64</option>
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335 <option value="32">32</option>
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336 </param>
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337 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
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338 <option value="64">64</option>
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339 <option value="32" selected="true">32</option>
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340 </param>
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341 <param type="boolean" name="zlib" label="Use zlib">
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342 </param>
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343 </when>
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344 </conditional>
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345
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346
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347 </inputs>
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348 <outputs>
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349 <data format="mzml" name="output">
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350 <change_format>
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351 <when input="output_type" value="mzXML" format="mzxml" />
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352 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
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353 <when input="output_type" value="ms2" format="ms2" />
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354 <when input="output_type" value="mgf" format="mgf" />
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355 </change_format>
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356 </data>
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357 </outputs>
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358
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359 <requirements>
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360 <requirement type="package">proteowizard</requirement>
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361 </requirements>
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362
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363 <help>
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364 **What it does**
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365
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366 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
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367
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368 You can view the original documentation here_.
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369
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370 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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371
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372 ------
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373
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374 **Citation**
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375
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376 For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
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377
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378 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
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379
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380 </help>
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381 </tool>
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