Mercurial > repos > galaxyp > msconvert

annotate msconvert_macros.xml @ 13:9b61227976d6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
author galaxyp
date Sat, 25 Jul 2020 18:13:58 -0400
parents cc5ccfa8ee28
children 3cf310697624
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <macros>
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2 <token name="@VERSION@">3.0.19052</token>
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3 <token name="@FULL_VERSION@">@VERSION@-089e81090</token>
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5 <xml name="msconvertCommand">
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 #import re
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9 #set $ext = $input.ext
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11 ## sanitize display name for use as temp filename
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12 #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier)
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13
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14 #if $ext == 'wiff':
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15 ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
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16 ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
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17 #set inputmask = "'"+$basename+"'"
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18 #elif $ext.endswith('tar'):
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19 ln -s '$input' '${basename}' &&
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20 tar xf '${basename}' &&
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21 #set basename = $os.path.splitext($basename)[0]
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22 #if $ext.startswith('waters'):
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23 #set inputmask = '*.raw'
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24 #elif $ext.startswith('agilent') or $ext.startswith('bruker'):
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25 #set inputmask = '*.d'
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26 #elif $ext.startswith('wiff'):
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27 #set inputmask = '*.wiff *.wiff2'
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28 #else
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29 #raise RuntimeError("Unrecognized type of tar (${ext})")
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30 #end if
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31 #else
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32 ln -s '$input' '${basename}' &&
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33 #set inputmask = "'"+$basename+"'"
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34 #end if
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35
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36 #if $data_processing.precursor_refinement.use_mzrefinement
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37 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
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38 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
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39 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
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40 #end if
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42 uid=`id -u` &&
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43 gid=`id -g` &&
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44
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45 wine64_anyuser msconvert ${inputmask}
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46 --outdir outputs
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47 --${output_type}
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49 #if $general_options.combineIonMobilitySpectra:
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50 --combineIonMobilitySpectra
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51 #end if
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53 #if $general_options.simAsSpectra:
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54 --simAsSpectra
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55 #end if
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57 #if $general_options.srmAsSpectra:
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58 --srmAsSpectra
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59 #end if
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61 #if $general_options.acceptZeroLengthSpectra:
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62 --acceptZeroLengthSpectra
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63 #end if
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65 #if $general_options.ignoreUnknownInstrumentError:
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66 --ignoreUnknownInstrumentError
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67 #end if
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69 #if $general_options.scan_summing.do_scan_summing:
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70 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
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71 #end if
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73 #if $general_options.multi_run_output.do_multi_run_output:
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74 #if len($general_options.multi_run_output.run_index_set) > 0
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75 --runIndexSet "
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76 #for $index in $general_options.multi_run_output.run_index_set
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77 [${index.from},${index.to}]
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78 #end for
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79 "
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80 #end if
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81 #else
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82 --runIndexSet $general_options.multi_run_output.runIndexSet
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83 #end if
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84
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85 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
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86 --stripLocationFromSourceFiles
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88 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
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89 #if $data_processing.peak_picking.pick_peaks
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90 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
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91 #end if
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92
9
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93 #if $data_processing.precursor_refinement.use_mzrefinement
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94 --filter "mzRefiner $input_ident_name
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95 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
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96 thresholdScore=$data_processing.precursor_refinement.thresholdScore
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97 thresholdValue=$data_processing.precursor_refinement.thresholdValue
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98 thresholdStep=$data_processing.precursor_refinement.thresholdStep
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99 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"
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100 #end if
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101
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102 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
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103 --filter "chargeStatePredictor
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104 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
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105 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
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106 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
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107 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
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108 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
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109 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
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110 --filter "turbocharger
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111 minCharge=$data_processing.charge_state_calculation.minCharge
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112 maxCharge=$data_processing.charge_state_calculation.maxCharge
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113 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
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114 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
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115 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
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116 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
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117 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
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118 #end if
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119
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120 #for threshold_entry in $data_processing.thresholds
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121 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
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122 #end for
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123
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124 #if $data_processing.filter_mz_windows.do_mzwindow_filter
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125 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
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126 #end if
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127
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128 #if $data_processing.etd_filtering.do_etd_filtering
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129 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
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130 $data_processing.etd_filtering.remove_charge_reduced
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131 $data_processing.etd_filtering.remove_neutral_loss
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132 $data_processing.etd_filtering.blanket_removal
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133 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
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134 #end if
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135
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136 #if $data_processing.ms2denoise.denoise
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137 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
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138 #end if
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139
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140 #if str($data_processing.ms2deisotope) == "true"
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141 --filter "MS2Deisotope"
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142 #end if
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143
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144 #if $data_processing.demultiplex.demultiplex_on
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145 --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize"
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146 #end if
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147
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148 ## SCAN INCLUSION/EXCLUSION FILTERS
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149 #if str($filtering.activation) != "false"
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150 --filter "activation $filtering.activation"
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151 #end if
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152
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153 #if len($filtering.indices) > 0
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154 --filter "index
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155 #for $index in $filtering.indices
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156 [${index.from},${index.to}]
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157 #end for
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158 "
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159 #end if
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160
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161 #if len($filtering.scan_numbers) > 0
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162 --filter "scanNumber
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163 #for $scan_number in $filtering.scan_numbers
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164 [${scan_number.from},${scan_number.to}]
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165 #end for
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166 "
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167 #end if
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168
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169 #if $filtering.strip_it.value
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170 --filter "stripIT"
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171 #end if
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172
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173 #if $filtering.filter_ms_levels.do_ms_level_filter
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174 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
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175 #end if
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176
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177 #if str($filtering.polarity) != "false"
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178 --filter "polarity $filtering.polarity"
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179 #end if
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180
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181 #if str($filtering.analyzer) != "false"
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182 --filter "analyzer $filtering.analyzer"
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183 #end if
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184
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185 ## OUTPUT ENCODING
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186 #set $mz_encoding = str($settings.mz_encoding)
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187 #set $intensity_encoding = str($settings.intensity_encoding)
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188 #if $mz_encoding == $intensity_encoding
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189 #if $mz_encoding == "64"
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190 --64
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191 #else
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192 --32
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193 #end if
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194 #else
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195 --mz${mz_encoding}
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196 --inten${intensity_encoding}
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197 #end if
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198
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199 #set binary_compression = str($settings.binary_compression)
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200 #if $binary_compression == "zlib"
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201 --zlib
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202 #else if $binary_compression == "numpressLinearPic"
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203 --numpressLinear --numpressPic
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204 #else if $binary_compression == "numpressLinearSlof"
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205 --numpressLinear --numpressSlof
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206 #else if $binary_compression == "numpressLinear"
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207 --numpressLinear
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208 #else if $binary_compression == "numpressPic"
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209 --numpressPic
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210 #else if $binary_compression == "numpressSlof"
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211 --numpressSlof
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212 #end if
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213
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214 #if $settings.gzip_compression
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215 --gzip
9
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216 #end if
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217
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218 #if $general_options.multi_run_output.do_multi_run_output == 'false':
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219 --outfile '${os.path.splitext($basename)[0]}'
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220 && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}'
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221 #else
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222 && sudo chown \$uid:\$gid 'outputs' -R
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223 && ls -la outputs/
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224 #end if
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225
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226 #if $data_processing.precursor_refinement.use_mzrefinement
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227 && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement'
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228 #end if
9
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229 ]]>
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230 </command>
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231 </xml>
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232
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233 <xml name="msconvertInputParameters">
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234 <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses proprietary vendor libraries; to run it you must agree to the vendor licenses. Read them at http://www.proteowizard.org/licenses.html">
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235 <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator>
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236 </param>
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237
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238 <param name="output_type" type="select" label="Output Type">
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239 <option value="mz5" selected="true">mz5</option>
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240 <option value="mzML">mzML</option>
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241 <option value="mzXML">mzXML</option>
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242 <option value="mgf">mgf</option>
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243 <option value="ms2">ms2</option>
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244 </param>
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245
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246 <section name="data_processing" title="Data Processing Filters">
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247 <conditional name="peak_picking">
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248 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
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249 <when value="false" />
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250 <when value="true">
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251 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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252 <option value="1">MS1 Only (1)</option>
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253 <option value="2">MS2 Only (2)</option>
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254 <option value="2-">MS2 and on (2-)</option>
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255 <option value="1-" selected="true">All Levels (1-)</option>
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256 </param>
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257 <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
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258 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
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259 <option value="cwt">CantWaiT - continuous wavelet transform</option>
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260 </param>
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261 </when>
9
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262 </conditional>
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263
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264 <conditional name="precursor_refinement">
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265 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
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266 <when value="false"></when>
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267 <when value="true">
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268 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
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269 <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+">
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270 <sanitizer>
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271 <valid initial="string.letters" />
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272 </sanitizer>
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273 </param>
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274 <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10.">
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275 <sanitizer>
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276 <valid initial="string.letters,string.digits">
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277 <add value="-" />
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278 </valid>
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279 </sanitizer>
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280 </param>
9
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281 <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
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282 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
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283 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
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284 <option value="1">MS1 Only (1)</option>
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285 <option value="2">MS2 Only (2)</option>
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286 <option value="2-">MS2 and on (2-)</option>
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287 <option value="1-" selected="true">All Levels (1-)</option>
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288 </param>
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289 </when>
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290 </conditional>
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291
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292 <conditional name="charge_state_calculation">
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293 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
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294 <option value="false">no</option>
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295 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
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296 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
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297 </param>
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298 <when value="false" />
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299 <when value="predictor">
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300 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
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301 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
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302 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
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303 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
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304 <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for &quot;known&quot; charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
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305 </when>
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306 <when value="turbocharger">
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307 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
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308 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
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309 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
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310 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
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311 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
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312 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
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313 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
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314 </when>
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315 </conditional>
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316
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317 <repeat name="thresholds" title="Filter by Threshold">
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318 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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319 <option value="count">Peak count</option>
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320 <option value="count-after-ties">Peak count (after ties)</option>
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321 <option value="absolute">Peak absolute intensity</option>
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322 <option value="bpi-relative">Fraction of base peak intensity</option>
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323 <option value="tic-relative">Fraction of total ion current</option>
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324 <option value="tic-fraction">Aggregate fraction of total ion current</option>
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325 </param>
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326 <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the &quot;Aggregated fraction&quot; method, peaks are accepted until this fraction of the TIC is accounted for." />
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327 <param type="select" label="Keep" name="orientation">
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328 <option value="most-intense">Most intense peaks</option>
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329 <option value="least-intense">Least intense peaks</option>
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330 </param>
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331 </repeat>
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332
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333 <conditional name="filter_mz_windows">
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334 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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335 <when value="false" />
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336 <when value="true">
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337 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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338 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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339 </when>
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340 </conditional>
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341
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342 <conditional name="etd_filtering">
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343 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
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344 <when value="false" />
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345 <when value="true">
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346 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
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347 <option value="true" selected="true">yes</option>
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348 <option value="false">no</option>
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349 </param>
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350 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
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351 <option value="true" selected="true">yes</option>
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352 <option value="false">no</option>
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353 </param>
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354 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
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355 <option value="true" selected="true">yes</option>
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356 <option value="false">no</option>
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357 </param>
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358 <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
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359 <option value="true" selected="true">yes</option>
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360 <option value="false">no</option>
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361 </param>
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362 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
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363 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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364 <option value="MZ" selected="true">mz</option>
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365 <option value="PPM">ppm</option>
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366 </param>
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367 </when>
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368 </conditional>
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369
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370 <conditional name="ms2denoise">
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371 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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372 <when value="true">
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373 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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374 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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375 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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376 </when>
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377 <when value="false" />
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378 </conditional>
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379
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380 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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381
13
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382 <conditional name="demultiplex">
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383 <param name="demultiplex_on" type="boolean" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)" />
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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384 <when value="true">
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385 <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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386 <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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387 <option value="MZ">mz</option>
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388 <option value="PPM" selected="true">ppm</option>
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389 </param>
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390 <param name="nnlsMaxIter" type="integer" label="Maximum iterations for NNLS solve" value="50"/>
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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391 <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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392 <param name="demuxBlockExtra" type="float" label="DemuxBlockExtra" help="Multiplier to expand or reduce the # of spectra considered when demultiplexing. If 0, a fully determined system of equations is built. If > 1.0, the number of rows included in the system is extended DemuxBlockExtra * (# scans in 1 duty cycle)" value="0"/>
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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393 <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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394 <param name="noSumNormalize" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Normalize sums" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
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395 <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
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396 <option value="none" selected="true">None</option>
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397 <option value="overlap_only">Overlap only</option>
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398 </param>
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399 <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
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400 <param name="noWeighting" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
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401 <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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402 </when>
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403 <when value="false" />
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404 </conditional>
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405
9
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406 </section>
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407
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408
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409 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
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410
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411 <param name="activation" type="select" label="Filter by Activation">
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412 <option value="false" selected="true">no</option>
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413 <option value="ETD">ETD</option>
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414 <option value="CID">CID</option>
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415 <option value="SA">SA</option>
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416 <option value="HCD">HCD</option>
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417 <option value="BIRD">BIRD</option>
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418 <option value="ECD">ECD</option>
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419 <option value="IRMPD">IRMPD</option>
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420 <option value="PD">PD</option>
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421 <option value="PSD">PSD</option>
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422 <option value="PQD">PQD</option>
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423 <option value="SID">SID</option>
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424 <option value="SORI">SORI</option>
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425 </param>
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426
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427 <repeat name="indices" title="Filter Scan Indices">
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428 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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429 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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430 </repeat>
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431
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432 <repeat name="scan_numbers" title="Filter Scan Numbers">
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433 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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434 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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435 </repeat>
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436
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437 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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438
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439 <conditional name="filter_ms_levels">
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440 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
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441 <when value="false" />
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442 <when value="true">
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443 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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444 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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445 </when>
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446 </conditional>
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447
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448 <param name="polarity" type="select" label="Filter by Polarity">
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449 <option value="false" selected="true">no</option>
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450 <option value="positive">positive</option>
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451 <option value="negative">negative</option>
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452 </param>
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453
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454 <param name="analyzer" type="select" label="Filter by Analyzer">
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455 <option value="false" selected="true">no</option>
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456 <option value="quad">Quadrupole</option>
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457 <option value="orbi">Orbitrap</option>
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458 <option value="FT">Fourier-transform</option>
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459 <option value="IT">Ion trap</option>
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460 <option value="TOF">Time of flight</option>
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461 </param>
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462 </section>
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463
10
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464 <section name="general_options" title="General Options">
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465 <param argument="--combineIonMobilitySpectra" type="boolean" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." />
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466
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467 <conditional name="scan_summing">
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468 <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" />
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469 <when value="false" />
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470 <when value="true">
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471 <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
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472 <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." />
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473 <param name="ionMobilityTol" type="float" label="Ion mobility tolerance" value="0.01" min="0" optional="true" help="Spectra with ion mobility values with a difference less than this tolerance are summed together. Only relevant for ion mobility spectra." />
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474 </when>
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475 </conditional>
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476
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477 <param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
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478 <param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
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479 <param argument="--acceptZeroLengthSpectra" type="boolean" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" />
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480 <param argument="--ignoreUnknownInstrumentError" type="boolean" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
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481
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482 <conditional name="multi_run_output">
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483 <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" />
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484 <when value="false">
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485 <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
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486 </when>
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487 <when value="true">
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488 <repeat name="run_index_set" title="Select runs for multi-run sources" help="For multi-run sources (e.g. WIFF), select only the specified run indices">
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489 <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" />
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490 <param name="to" type="integer" label="Run Index To" value="0" min="0" optional="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
491 </repeat>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
492 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
493 </conditional>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
494 </section>
9
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galaxyp
parents:
diff changeset
495
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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496 <section name="settings" title="Output Encoding Settings">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
497 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
498 <option value="64" selected="true">64</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
499 <option value="32">32</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
500 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
501 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
502 <option value="64">64</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
503 <option value="32" selected="true">32</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
504 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
505 <param type="select" name="binary_compression" label="Binary data compression">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
506 <option value="false">None</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
507 <option value="zlib" selected="true">zlib</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
508 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
509 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
510 <option value="numpressLinear">numpressLinear only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
511 <option value="numpressPic">numpressPic only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
512 <option value="numpressSlof">numpressSlof only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
513 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
514 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
515 </section>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
516 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
517
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
518 <xml name="msconvertOutput">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
519 <outputs>
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
520 <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" >
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
521 <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter>
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
522 <change_format>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
523 <when input="output_type" value="mz5" format="mz5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
524 <when input="output_type" value="mzXML" format="mzxml" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
525 <when input="output_type" value="ms2" format="ms2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
526 <when input="output_type" value="mgf" format="mgf" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
527 </change_format>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
528 </data>
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
529 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
530 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
531 </data>
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
532 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
533 <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
534 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
535 </collection>
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
536 </outputs>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
537 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
538
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
539
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
540 <xml name="msconvert_tests">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
541 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
542 <param name="input" value="small.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
543 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
544 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
545 <param name="pick_peaks" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
546 <param name="pick_peaks_algorithm" value="cwt" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
547 <param name="pick_peaks_ms_levels" value="1-" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
548 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
549 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
550 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
551 <param name="input" value="small.RAW" ftype="thermo.raw" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
552 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
553 <param name="output_type" value="mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
554 <param name="pick_peaks" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
555 <param name="pick_peaks_algorithm" value="vendor" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
556 <param name="pick_peaks_ms_levels" value="1-" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
557 <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
558 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
559 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
560 <param name="input" value="ThyroglobMRM000003.d.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
561 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
562 <param name="output_type" value="mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
563 <param name="combineIonMobilitySpectra" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
564 <param name="do_scan_summing" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
565 <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
566 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
567 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
568 <param name="input" value="MassLynxTest.raw.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
569 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
570 <param name="output_type" value="mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
571 <output name="output" file="MassLynxTest.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
572 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
573 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
574 <param name="input" value="AgilentMassHunterTest.d.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
575 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
576 <param name="output_type" value="mzXML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
577 <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
578 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
579 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
580 <param name="input" value="BrukerBafTest.d.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
581 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
582 <param name="output_type" value="mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
583 <param name="pick_peaks" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
584 <param name="pick_peaks_algorithm" value="vendor" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
585 <param name="pick_peaks_ms_levels" value="1-" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
586 <output name="output" file="BrukerBafTest.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
587 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
588 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
589 <param name="input" value="SciexTest.wiff.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
590 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
591 <param name="output_type" value="mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
592 <param name="do_multi_run_output" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
593 <param name="runIndexSet" value="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
594 <output name="output" file="SciexTest-HPINalone.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
595 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
596 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
597 <param name="input" value="SciexTest.wiff.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
598 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
599 <param name="output_type" value="mzXML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
600 <param name="do_multi_run_output" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
601 <param name="runIndexSet" value="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
602 <param name="indices_0|from" value="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
603 <param name="indices_0|to" value="499" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
604 <param name="srmAsSpectra" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
605 <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
606 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
607 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
608 <param name="input" value="SciexTest.wiff.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
609 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
610 <param name="output_type" value="mzXML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
611 <param name="do_multi_run_output" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
612 <param name="runIndexSet" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
613 <param name="indices_0|from" value="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
614 <param name="indices_0|to" value="499" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
615 <param name="srmAsSpectra" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
616 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
617 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
618 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
619 <param name="input" value="SciexTest.wiff.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
620 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
621 <param name="output_type" value="mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
622 <param name="do_multi_run_output" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
623 <param name="run_index_set_0|from" value="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
624 <param name="run_index_set_0|to" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
625 <output_collection name="multi_run_output_list" type="list">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
626 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
627 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
628 </output_collection>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
629 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
630 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
631 <param name="input" value="SciexTest.wiff.tar" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
632 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
633 <param name="output_type" value="mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
634 <param name="do_multi_run_output" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
635 <output_collection name="multi_run_output_list" type="list">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
636 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
637 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
638 </output_collection>
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
639 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
640
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
641 <!-- this data file only has profile MS1, so the result is the same -->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
642 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
643 <param name="input" value="small.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
644 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
645 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
646 <param name="pick_peaks" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
647 <param name="pick_peaks_algorithm" value="cwt" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
648 <param name="pick_peaks_ms_levels" value="1" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
649 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
650 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
651 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
652 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
653 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
654 <param name="output_type" value="mz5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
655 <param name="mz_encoding" value="64" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
656 <param name="intensity_encoding" value="64" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
657 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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diff changeset
658 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
659 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
660 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
661 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
662 <param name="output_type" value="mzXML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
663 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
664 <param name="intensity_encoding" value="32" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
665 <output name="output" file="small-zlib-32.mzXML" lines_diff="6" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
666 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
667 <!-- TODO: how to test gzipped output?
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
668 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
669 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
670 <param name="output_type" value="mzXML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
671 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
672 <param name="intensity_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
673 <param name="binary_compression" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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674 <param name="gzip_compression" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
675 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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diff changeset
676 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
677 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
678 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
679 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
680 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
681 <param name="intensity_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
682 <param name="binary_compression" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
683 <param name="gzip_compression" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
684 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
685 </test>-->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
686
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
687 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
688 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
689 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
690 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
691 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
692 <output name="output" file="small-numpressLP.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
693 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
694
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
695 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
696 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
697 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
698 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
699 <param name="binary_compression" value="numpressLinearSlof" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
700 <output name="output" file="small-numpressLS.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
701 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
702
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
703 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
704 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
705 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
706 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
707 <param name="binary_compression" value="numpressLinear" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
708 <output name="output" file="small-numpressL.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
709 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
710
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
711 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
712 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
713 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
714 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
715 <param name="binary_compression" value="numpressPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
716 <output name="output" file="small-numpressP.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
717 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
718
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
719 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
720 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
721 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
722 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
723 <param name="binary_compression" value="numpressSlof" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
724 <output name="output" file="small-numpressS.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
725 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
726
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
727 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
728 <param name="input" value="Rpal_01.mz5" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
729 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
730 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
731 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
732 <param name="use_mzrefinement" value="true" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
733 <param name="input_ident" value="Rpal_01.pepXML" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
734 <param name="thresholdScore" value="mvh" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
735 <param name="thresholdValue" value="40-" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
736 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
737 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
738 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
739
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
740 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
741 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
742 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
743 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
744 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
745 <param name="charge_state_calculation_method" value="predictor" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
746 <param name="predictor_overrideExistingCharge" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
747 <param name="minMultipleCharge" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
748 <param name="maxMultipleCharge" value="5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
749 <param name="singleChargeFractionTIC" value="0.95" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
750 <param name="maxKnownCharge" value="8" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
751 <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
752 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
753 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
754 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
755 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
756 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
757 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
758 <param name="charge_state_calculation_method" value="turbocharger" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
759 <param name="minCharge" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
760 <param name="maxCharge" value="5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
761 <param name="precursorsBefore" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
762 <param name="precursorsAfter" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
763 <param name="halfIsoWidth" value="1.5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
764 <param name="defaultMinCharge" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
765 <param name="defaultMaxCharge" value="5" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
766 <output name="output" file="small-turbocharger.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
767 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
768 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
769 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
770 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
771 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
772 <param name="do_etd_filtering" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
773 <param name="remove_precursor" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
774 <param name="remove_charge_reduced" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
775 <param name="remove_neutral_loss" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
776 <param name="blanket_removal" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
777 <param name="matching_tolerance" value="50" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
778 <param name="matching_tolerance_units" value="ppm" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
779 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
780 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
781 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
782 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
783 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
784 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
785 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
786 <param name="thresholds_0|threshold_type" value="count" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
787 <param name="thresholds_0|value" value="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
788 <param name="thresholds_0|orientation" value="most-intense" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
789 <param name="thresholds_1|threshold_type" value="absolute" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
790 <param name="thresholds_1|value" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
791 <param name="thresholds_1|orientation" value="most-intense" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
792 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
793 <output name="output" file="small-threshold.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
794 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
795 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
796 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
797 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
798 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
799 <param name="do_mzwindow_filter" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
800 <param name="mz_window_from" value="420" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
801 <param name="mz_window_to" value="840" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
802 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
803 <output name="output" file="small-mzWindow.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
804 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
805 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
806 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
807 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
808 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
809 <param name="denoise" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
810 <param name="num_peaks" value="10" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
811 <param name="window_width" value="40" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
812 <param name="relax" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
813 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
814 <output name="output" file="small-denoise.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
815 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
816 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
817 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
818 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
819 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
820 <param name="ms2deisotope" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
821 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
822 <output name="output" file="small-deisotope.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
823 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
824 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
825 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
826 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
827 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
828 <param name="activation" value="CID" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
829 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
830 <output name="output" file="small-activation.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
831 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
832 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
833 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
834 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
835 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
836 <param name="indices_0|from" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
837 <param name="indices_0|to" value="4" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
838 <param name="indices_1|from" value="10" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
839 <param name="indices_1|to" value="10" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
840 <param name="indices_2|from" value="13" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
841 <param name="indices_2|to" value="15" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
842 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
843 <output name="output" file="small-index-filter.mzML" lines_diff="32" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
844 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
845 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
846 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
847 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
848 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
849 <param name="strip_it" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
850 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
851 <output name="output" file="small-strip-it.mzML" lines_diff="100" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
852 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
853 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
854 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
855 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
856 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
857 <param name="do_ms_level_filter" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
858 <param name="ms_level_from" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
859 <param name="ms_level_to" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
860 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
861 <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
862 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
863 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
864 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
865 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
866 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
867 <param name="polarity" value="positive" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
868 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
869 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
870 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
871 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
872 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
873 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
874 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
875 <param name="analyzer" value="IT" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
876 <param name="binary_compression" value="numpressLinearPic" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
877 <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
878 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
879 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
880 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
881 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
882 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
883 <param name="scan_numbers_0|from" value="3" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
884 <param name="scan_numbers_0|to" value="5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
885 <param name="scan_numbers_1|from" value="11" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
886 <param name="scan_numbers_1|to" value="11" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
887 <param name="scan_numbers_2|from" value="14" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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888 <param name="scan_numbers_2|to" value="16" />
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889 <param name="binary_compression" value="numpressLinearPic" />
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890 <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->
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891 </test>
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892 <!--<test>
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893 <param name="input" value="small.mzML" />
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894 <param name="output_type" value="mzML" />
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895 <param name="binary_compression" value="numpressLinearPic" />
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896 <output name="output" file="small-deisotope-poisson.mzML" />
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897 </test>-->
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898 </xml>
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899 <xml name="msconvert_help">
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900 **What it does**
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901
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902 Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.
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903
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904 You can view the original documentation here_.
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905
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906 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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907 </xml>
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908
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909 <xml name="citations">
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910 <citations>
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911 <citation type="doi">10.1093/bioinformatics/btn323</citation>
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912 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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913 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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914 </citations>
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915 </xml>
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916
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917 </macros>