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1 <macros>
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2 <xml name="generic_requirements">
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3 <requirements>
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4 <requirement type="package" version="3.0.9016">proteowizard</requirement>
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5 </requirements>
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6 </xml>
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7 <token name="@VERSION@">3.0</token>
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8
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9 <xml name="msconvertCommand">
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10 <command interpreter="python">
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11 <![CDATA[
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12 #import re
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13 #set $ext = $input.ext
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14 msconvert_wrapper.py
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15 #if $ext == 'wiff':
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16 #set basename = 'absciex'
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17 #if hasattr($input, 'display_name')
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18 #set basename = $re.sub('\W','_',$input.display_name)
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19 #end if
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20 --input=${input.extra_files_path}/wiff
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21 --input_name='${basename}.wiff
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22 --implicit=${input.extra_files_path}/wiff_scan
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23 --input=${input.extra_files_path}/wiff_scan
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24 --input_name='${basename}.wiff.scan
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25 #else
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26 --input=${input}
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27 #if hasattr($input, 'display_name')
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28 --input_name='${input.display_name}'
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29 #end if
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30 #end if
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31 --output=${output}
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32 ## BEGIN_VERSION_DEFAULT
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33 --fromextension=$ext
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34 ## END_VERSION_DEFAULT
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35 --toextension=${output_type}
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36
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37 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
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38 #if $data_processing.precursor_refinement.use_mzrefinement
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39 #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name)
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40 #if $data_processing.precursor_refinement.input_ident.ext == 'mzid':
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41 #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name)
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42 #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml':
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43 #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name)
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44 #end if
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45 --ident=$data_processing.precursor_refinement.input_ident
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46 --ident_name=$input_ident_name
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47 --refinement=$output_refinement
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48 --filter "mzRefiner $input_ident_name
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49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
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50 thresholdScore=$data_processing.precursor_refinement.thresholdScore
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51 thresholdValue=$data_processing.precursor_refinement.thresholdValue
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52 thresholdStep=$data_processing.precursor_refinement.thresholdStep
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53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
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54 #end if
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55
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56 #if $data_processing.peak_picking.pick_peaks
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57 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
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58 #end if
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59
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60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
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61 --filter "chargeStatePredictor
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62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
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63 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
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64 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
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65 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
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66 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
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67 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
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68 --filter "turbocharger
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69 minCharge=$data_processing.charge_state_calculation.minCharge
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70 maxCharge=$data_processing.charge_state_calculation.maxCharge
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71 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
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72 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
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73 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
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74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
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75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
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76 #end if
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77
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78 #for threshold_entry in $data_processing.thresholds
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79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
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80 #end for
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81
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82 #if $data_processing.filter_mz_windows.do_mzwindow_filter
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83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
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84 #end if
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85
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86 #if $data_processing.etd_filtering.do_etd_filtering
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87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
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88 $data_processing.etd_filtering.remove_charge_reduced
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89 $data_processing.etd_filtering.remove_neutral_loss
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90 $data_processing.etd_filtering.blanket_removal
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91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
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92 #end if
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93
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94 #if $data_processing.ms2denoise.denoise
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95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
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96 #end if
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97
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98 #if str($data_processing.ms2deisotope) == "true"
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99 --filter "MS2Deisotope"
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100 #end if
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101
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102
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103 ## SCAN INCLUSION/EXCLUSION FILTERS
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104 #if str($filtering.activation) != "false"
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105 --filter "activation $filtering.activation"
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106 #end if
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107
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108 #if len($filtering.indices) > 0
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109 --filter "index
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110 #for $index in $filtering.indices
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111 [${index.from},${index.to}]
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112 #end for
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113 "
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114 #end if
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115
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116 #if len($filtering.scan_numbers) > 0
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117 --filter "scanNumber
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118 #for $scan_number in $filtering.scan_numbers
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119 [${scan_number.from},${scan_number.to}]
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120 #end for
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121 "
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122 #end if
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123
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124 #if $filtering.strip_it.value
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125 --filter "stripIT"
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126 #end if
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127
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128 #if $filtering.filter_ms_levels.do_ms_level_filter
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129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
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130 #end if
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131
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132 #if str($filtering.polarity) != "false"
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133 --filter "polarity $filtering.polarity"
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134 #end if
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135
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136 #if str($filtering.analyzer) != "false"
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137 --filter "analyzer $filtering.analyzer"
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138 #end if
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139
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140 ## OUTPUT ENCODING
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141 --
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142 #set $mz_encoding = str($settings.mz_encoding)
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143 #set $intensity_encoding = str($settings.intensity_encoding)
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144 #if $mz_encoding == $intensity_encoding
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145 #if $mz_encoding == "64"
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146 --64
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147 #else
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148 --32
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149 #end if
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150 #else
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151 --mz${mz_encoding}
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152 --inten${intensity_encoding}
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153 #end if
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154
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155 #set binary_compression = str($settings.binary_compression)
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156 #if $binary_compression == "zlib"
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157 --zlib
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158 #else if $binary_compression == "numpressLinearPic"
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159 --numpressLinear --numpressPic
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160 #else if $binary_compression == "numpressLinearSlof"
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161 --numpressLinear --numpressSlof
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162 #else if $binary_compression == "numpressLinear"
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163 --numpressLinear
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164 #else if $binary_compression == "numpressPic"
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165 --numpressPic
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166 #else if $binary_compression == "numpressSlof"
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167 --numpressSlof
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168 #end if
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169
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170 #if $settings.gzip_compression
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171 --gzip
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172 #end if
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173
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174 ]]>
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175 </command>
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176 </xml>
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177
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178 <xml name="msconvertInputParameters">
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179 <param name="output_type" type="select" label="Output Type">
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180 <option value="mz5" selected="true">mz5</option>
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181 <option value="mzML">mzML</option>
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182 <option value="mzXML">mzXML</option>
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183 <option value="mgf">mgf</option>
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184 <option value="ms2">ms2</option>
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185 </param>
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186
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187 <section name="data_processing" title="Data Processing Filters">
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188
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189 <conditional name="peak_picking">
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190 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
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191 <when value="false" />
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192 <when value="true">
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193 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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194 <option value="1">MS1 Only (1)</option>
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195 <option value="2">MS2 Only (2)</option>
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196 <option value="2-">MS2 and on (2-)</option>
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197 <option value="1-" selected="true">All Levels (1-)</option>
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198 </param>
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199 <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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200 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
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201 <option value="cwt">CantWaiT - continuous wavelet transform</option>
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202 </param>
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203 </when>
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204 </conditional>
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205
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206 <conditional name="precursor_refinement" title="MZRefinery Precursor Refinement" expanded="true">
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207 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
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208 <when value="false"></when>
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209 <when value="true">
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210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
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211 <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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212 <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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213 <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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214 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
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215 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
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216 <option value="1">MS1 Only (1)</option>
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217 <option value="2">MS2 Only (2)</option>
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218 <option value="2-">MS2 and on (2-)</option>
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219 <option value="1-" selected="true">All Levels (1-)</option>
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220 </param>
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221 </when>
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222 </conditional>
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223
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224 <conditional name="charge_state_calculation">
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225 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
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226 <option value="false">no</option>
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227 <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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228 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
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229 </param>
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230 <when value="false" />
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231 <when value="predictor">
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232 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
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233 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
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234 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
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235 <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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236 <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for "known" 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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237 </when>
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238 <when value="turbocharger">
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239 <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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240 <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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241 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
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242 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
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243 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
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244 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
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245 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
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246 </when>
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247 </conditional>
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248
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249 <repeat name="thresholds" title="Filter by Threshold">
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250 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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251 <option value="count">Peak count</option>
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252 <option value="count-after-ties">Peak count (after ties)</option>
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253 <option value="absolute">Peak absolute intensity</option>
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254 <option value="bpi-relative">Fraction of base peak intensity</option>
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255 <option value="tic-relative">Fraction of total ion current</option>
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256 <option value="tic-fraction">Aggregate fraction of total ion current</option>
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257 </param>
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258 <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 "Aggregated fraction" method, peaks are accepted until this fraction of the TIC is accounted for." />
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259 <param type="select" label="Keep" name="orientation">
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260 <option value="most-intense">Most intense peaks</option>
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261 <option value="least-intense">Least intense peaks</option>
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262 </param>
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263 </repeat>
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264
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265 <conditional name="filter_mz_windows">
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266 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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267 <when value="false" />
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268 <when value="true">
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269 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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270 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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271 </when>
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272 </conditional>
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273
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274 <conditional name="etd_filtering">
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275 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
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276 <when value="false" />
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277 <when value="true">
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278 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
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279 <option value="true" selected="true">yes</option>
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280 <option value="false">no</option>
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281 </param>
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282 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
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283 <option value="true" selected="true">yes</option>
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284 <option value="false">no</option>
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285 </param>
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286 <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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287 <option value="true" selected="true">yes</option>
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288 <option value="false">no</option>
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289 </param>
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290 <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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291 <option value="true" selected="true">yes</option>
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292 <option value="false">no</option>
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293 </param>
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294 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
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295 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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296 <option value="MZ" selected="true">mz</option>
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297 <option value="PPM">ppm</option>
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298 </param>
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299 </when>
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300 </conditional>
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301
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302 <conditional name="ms2denoise">
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303 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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304 <when value="true">
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305 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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306 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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307 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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308 </when>
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309 <when value="false" />
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310 </conditional>
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311
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312 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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313
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314 </section>
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315
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316
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317 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
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318
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319 <param name="activation" type="select" label="Filter by Activation">
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320 <option value="false" selected="true">no</option>
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321 <option value="ETD">ETD</option>
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322 <option value="CID">CID</option>
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323 <option value="SA">SA</option>
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|
|
324 <option value="HCD">HCD</option>
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|
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325 <option>BIRD</option>
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|
|
326 <option>ECD</option>
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|
|
327 <option>IRMPD</option>
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328 <option>PD</option>
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329 <option>PSD</option>
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|
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330 <option>PQD</option>
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|
331 <option>SID</option>
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332 <option>SORI</option>
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|
333 </param>
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334
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|
|
335 <repeat name="indices" title="Filter Scan Indices">
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|
|
336 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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|
|
337 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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|
|
338 </repeat>
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|
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339
|
|
|
340 <repeat name="scan_numbers" title="Filter Scan Numbers">
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|
|
341 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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|
|
342 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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|
|
343 </repeat>
|
|
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344
|
|
|
345 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
|
|
|
346
|
|
|
347 <conditional name="filter_ms_levels">
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|
|
348 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
|
|
|
349 <when value="false" />
|
|
|
350 <when value="true">
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|
|
351 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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|
|
352 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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|
|
353 </when>
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|
|
354 </conditional>
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|
|
355
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|
|
356 <param name="polarity" type="select" label="Filter by Polarity">
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|
357 <option value="false" selected="true">no</option>
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|
|
358 <option value="positive">positive</option>
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|
359 <option value="negative">negative</option>
|
|
|
360 </param>
|
|
|
361
|
|
|
362 <param name="analyzer" type="select" label="Filter by Analyzer">
|
|
|
363 <option value="false" selected="true">no</option>
|
|
|
364 <option value="quad">Quadrupole</option>
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|
|
365 <option value="orbi">Orbitrap</option>
|
|
|
366 <option value="FT">Fourier-transform</option>
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|
|
367 <option value="IT">Ion trap</option>
|
|
|
368 <option value="TOF">Time of flight</option>
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|
|
369 </param>
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|
|
370 </section>
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|
|
371
|
|
|
372
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|
|
373 <section name="settings" title="Output Encoding Settings">
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|
374 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
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|
|
375 <option value="64" selected="true">64</option>
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|
|
376 <option value="32">32</option>
|
|
|
377 </param>
|
|
|
378 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
|
|
|
379 <option value="64">64</option>
|
|
|
380 <option value="32" selected="true">32</option>
|
|
|
381 </param>
|
|
|
382 <param type="select" name="binary_compression" label="Binary data compression">
|
|
|
383 <option value="false">None</option>
|
|
|
384 <option value="zlib" selected="true">zlib</option>
|
|
|
385 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
|
|
|
386 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
|
|
|
387 <option value="numpressLinear">numpressLinear only</option>
|
|
|
388 <option value="numpressPic">numpressPic only</option>
|
|
|
389 <option value="numpressSlof">numpressSlof only</option>
|
|
|
390 </param>
|
|
|
391 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
|
|
|
392 </section>
|
|
|
393 </xml>
|
|
|
394
|
|
|
395 <xml name="msconvertOutput">
|
|
|
396 <outputs>
|
|
|
397 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
|
|
|
398 <change_format>
|
|
|
399 <when input="output_type" value="mz5" format="mz5" />
|
|
|
400 <when input="output_type" value="mzXML" format="mzxml" />
|
|
|
401 <when input="output_type" value="ms2" format="ms2" />
|
|
|
402 <when input="output_type" value="mgf" format="mgf" />
|
|
|
403 </change_format>
|
|
|
404 </data>
|
|
|
405 <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
|
|
|
406 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
|
|
|
407 </data>
|
|
|
408 </outputs>
|
|
|
409 </xml>
|
|
|
410
|
|
|
411
|
|
|
412 <xml name="msconvert_tests">
|
|
|
413 <test>
|
|
|
414 <param name="input" value="small.mzML" />
|
|
|
415 <param name="output_type" value="mzML" />
|
|
|
416 <param name="pick_peaks" value="true" />
|
|
|
417 <param name="pick_peaks_algorithm" value="cwt" />
|
|
|
418 <param name="pick_peaks_ms_levels" value="1-" />
|
|
|
419 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
|
|
|
420 </test>
|
|
|
421
|
|
|
422 <!-- this data file only has profile MS1, so the result is the same -->
|
|
|
423 <test>
|
|
|
424 <param name="input" value="small.mzML" />
|
|
|
425 <param name="output_type" value="mzML" />
|
|
|
426 <param name="pick_peaks" value="true" />
|
|
|
427 <param name="pick_peaks_algorithm" value="cwt" />
|
|
|
428 <param name="pick_peaks_ms_levels" value="1" />
|
|
|
429 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
|
|
|
430 </test>
|
|
|
431 <test>
|
|
|
432 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
433 <param name="output_type" value="mz5" />
|
|
|
434 <param name="mz_encoding" value="64" />
|
|
|
435 <param name="intensity_encoding" value="64" />
|
|
|
436 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
|
|
|
437 </test>
|
|
|
438 <test>
|
|
|
439 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
440 <param name="output_type" value="mzXML" />
|
|
|
441 <param name="mz_encoding" value="32" />
|
|
|
442 <param name="intensity_encoding" value="32" />
|
|
|
443 <output name="output" file="small-zlib-32.mzXML" />
|
|
|
444 </test>
|
|
|
445 <!-- TODO: how to test gzipped output?
|
|
|
446 <test>
|
|
|
447 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
448 <param name="output_type" value="mzXML" />
|
|
|
449 <param name="mz_encoding" value="32" />
|
|
|
450 <param name="intensity_encoding" value="32" />
|
|
|
451 <param name="binary_compression" value="false" />
|
|
|
452 <param name="gzip_compression" value="true" />
|
|
|
453 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
|
|
|
454 </test>
|
|
|
455 <test>
|
|
|
456 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
457 <param name="output_type" value="mzML" />
|
|
|
458 <param name="mz_encoding" value="32" />
|
|
|
459 <param name="intensity_encoding" value="32" />
|
|
|
460 <param name="binary_compression" value="false" />
|
|
|
461 <param name="gzip_compression" value="true" />
|
|
|
462 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
|
|
|
463 </test>-->
|
|
|
464
|
|
|
465 <test>
|
|
|
466 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
467 <param name="output_type" value="mzML" />
|
|
|
468 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
469 <output name="output" file="small-numpressLP.mzML" />
|
|
|
470 </test>
|
|
|
471
|
|
|
472 <test>
|
|
|
473 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
474 <param name="output_type" value="mzML" />
|
|
|
475 <param name="binary_compression" value="numpressLinearSlof" />
|
|
|
476 <output name="output" file="small-numpressLS.mzML" />
|
|
|
477 </test>
|
|
|
478
|
|
|
479 <test>
|
|
|
480 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
481 <param name="output_type" value="mzML" />
|
|
|
482 <param name="binary_compression" value="numpressLinear" />
|
|
|
483 <output name="output" file="small-numpressL.mzML" />
|
|
|
484 </test>
|
|
|
485
|
|
|
486 <test>
|
|
|
487 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
488 <param name="output_type" value="mzML" />
|
|
|
489 <param name="binary_compression" value="numpressPic" />
|
|
|
490 <output name="output" file="small-numpressP.mzML" />
|
|
|
491 </test>
|
|
|
492
|
|
|
493 <test>
|
|
|
494 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
495 <param name="output_type" value="mzML" />
|
|
|
496 <param name="binary_compression" value="numpressSlof" />
|
|
|
497 <output name="output" file="small-numpressS.mzML" />
|
|
|
498 </test>
|
|
|
499
|
|
|
500 <test>
|
|
|
501 <param name="input" value="Rpal_01.mz5" />
|
|
|
502 <param name="output_type" value="mzML" />
|
|
|
503 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
504 <param name="use_mzrefinement" value="true" />
|
|
|
505 <param name="input_ident" value="Rpal_01.pepXML.gz" />
|
|
|
506 <param name="thresholdScore" value="mvh" />
|
|
|
507 <param name="thresholdValue" value="40-" />
|
|
|
508 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
|
|
|
509 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
|
|
|
510 </test>
|
|
|
511
|
|
|
512 <test>
|
|
|
513 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
514 <param name="output_type" value="mzML" />
|
|
|
515 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
516 <param name="charge_state_calculation_method" value="predictor" />
|
|
|
517 <param name="predictor_overrideExistingCharge" value="true" />
|
|
|
518 <param name="minMultipleCharge" value="2" />
|
|
|
519 <param name="maxMultipleCharge" value="5" />
|
|
|
520 <param name="singleChargeFractionTIC" value="0.95" />
|
|
|
521 <param name="maxKnownCharge" value="8" />
|
|
|
522 <output name="output" file="small-chargeStatePredictor.mzML" />
|
|
|
523 </test>
|
|
|
524 <test>
|
|
|
525 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
526 <param name="output_type" value="mzML" />
|
|
|
527 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
528 <param name="charge_state_calculation_method" value="turbocharger" />
|
|
|
529 <param name="minCharge" value="1" />
|
|
|
530 <param name="maxCharge" value="5" />
|
|
|
531 <param name="precursorsBefore" value="1" />
|
|
|
532 <param name="precursorsAfter" value="1" />
|
|
|
533 <param name="halfIsoWidth" value="1.5" />
|
|
|
534 <param name="defaultMinCharge" value="1" />
|
|
|
535 <param name="defaultMaxCharge" value="5" />
|
|
|
536 <output name="output" file="small-turbocharger.mzML" />
|
|
|
537 </test>
|
|
|
538 <test>
|
|
|
539 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
|
|
|
540 <param name="output_type" value="mzML" />
|
|
|
541 <param name="do_etd_filtering" value="true" />
|
|
|
542 <param name="remove_precursor" value="true" />
|
|
|
543 <param name="remove_charge_reduced" value="true" />
|
|
|
544 <param name="remove_neutral_loss" value="false" />
|
|
|
545 <param name="blanket_removal" value="false" />
|
|
|
546 <param name="matching_tolerance" value="50" />
|
|
|
547 <param name="matching_tolerance_units" value="ppm" />
|
|
|
548 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
549 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
|
|
|
550 </test>
|
|
|
551 <test>
|
|
|
552 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
553 <param name="output_type" value="mzML" />
|
|
|
554 <param name="thresholds_0|threshold_type" value="count" />
|
|
|
555 <param name="thresholds_0|value" value="100" />
|
|
|
556 <param name="thresholds_0|orientation" value="most-intense" />
|
|
|
557 <param name="thresholds_1|threshold_type" value="absolute" />
|
|
|
558 <param name="thresholds_1|value" value="1" />
|
|
|
559 <param name="thresholds_1|orientation" value="most-intense" />
|
|
|
560 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
561 <output name="output" file="small-threshold.mzML" />
|
|
|
562 </test>
|
|
|
563 <test>
|
|
|
564 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
565 <param name="output_type" value="mzML" />
|
|
|
566 <param name="do_mzwindow_filter" value="true" />
|
|
|
567 <param name="mz_window_from" value="420" />
|
|
|
568 <param name="mz_window_to" value="840" />
|
|
|
569 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
570 <output name="output" file="small-mzWindow.mzML" />
|
|
|
571 </test>
|
|
|
572 <test>
|
|
|
573 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
574 <param name="output_type" value="mzML" />
|
|
|
575 <param name="denoise" value="true" />
|
|
|
576 <param name="num_peaks" value="10" />
|
|
|
577 <param name="window_width" value="40" />
|
|
|
578 <param name="relax" value="false" />
|
|
|
579 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
580 <output name="output" file="small-denoise.mzML" />
|
|
|
581 </test>
|
|
|
582 <test>
|
|
|
583 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
584 <param name="output_type" value="mzML" />
|
|
|
585 <param name="ms2deisotope" value="true" />
|
|
|
586 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
587 <output name="output" file="small-deisotope.mzML" />
|
|
|
588 </test>
|
|
|
589 <test>
|
|
|
590 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
591 <param name="output_type" value="mzML" />
|
|
|
592 <param name="activation" value="CID" />
|
|
|
593 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
594 <output name="output" file="small-activation.mzML" />
|
|
|
595 </test>
|
|
|
596 <test>
|
|
|
597 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
598 <param name="output_type" value="mzML" />
|
|
|
599 <param name="indices_0|from" value="2" />
|
|
|
600 <param name="indices_0|to" value="4" />
|
|
|
601 <param name="indices_1|from" value="10" />
|
|
|
602 <param name="indices_1|to" value="10" />
|
|
|
603 <param name="indices_2|from" value="13" />
|
|
|
604 <param name="indices_2|to" value="15" />
|
|
|
605 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
606 <output name="output" file="small-index-filter.mzML" />
|
|
|
607 </test>
|
|
|
608 <test>
|
|
|
609 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
610 <param name="output_type" value="mzML" />
|
|
|
611 <param name="strip_it" value="true" />
|
|
|
612 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
613 <output name="output" file="small-strip-it.mzML" />
|
|
|
614 </test>
|
|
|
615 <test>
|
|
|
616 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
617 <param name="output_type" value="mzML" />
|
|
|
618 <param name="do_ms_level_filter" value="true" />
|
|
|
619 <param name="ms_level_from" value="2" />
|
|
|
620 <param name="ms_level_to" value="2" />
|
|
|
621 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
622 <output name="output" file="small-ms-level-filter.mzML" />
|
|
|
623 </test>
|
|
|
624 <test>
|
|
|
625 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
626 <param name="output_type" value="mzML" />
|
|
|
627 <param name="polarity" value="positive" />
|
|
|
628 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
629 <output name="output" file="small-polarity-filter.mzML" />
|
|
|
630 </test>
|
|
|
631 <test>
|
|
|
632 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
633 <param name="output_type" value="mzML" />
|
|
|
634 <param name="analyzer" value="IT" />
|
|
|
635 <param name="binary_compression" value="numpressLinearPic" />
|
|
|
636 <output name="output" file="small-analyzer-filter.mzML" />
|
|
|
637 </test>
|
|
|
638 <test>
|
|
|
639 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
|
|
|
640 <param name="output_type" value="mzML" />
|
|
|
641 <param name="scan_numbers_0|from" value="3" />
|
|
|
642 <param name="scan_numbers_0|to" value="5" />
|
|
|
643 <param name="scan_numbers_1|from" value="11" />
|
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644 <param name="scan_numbers_1|to" value="11" />
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645 <param name="scan_numbers_2|from" value="14" />
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646 <param name="scan_numbers_2|to" value="16" />
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647 <param name="binary_compression" value="numpressLinearPic" />
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648 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
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649 </test>
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650 <!--<test>
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651 <param name="input" value="small.mzML" />
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652 <param name="output_type" value="mzML" />
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653 <param name="binary_compression" value="numpressLinearPic" />
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654 <output name="output" file="small-deisotope-poisson.mzML" />
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655 </test>-->
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656 </xml>
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657 <xml name="msconvert_help">
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658 **What it does**
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659
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660 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
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661
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662 You can view the original documentation here_.
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663
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664 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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665 </xml>
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666
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667 <xml name="citations">
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668 <citations>
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669 <citation type="doi">10.1093/bioinformatics/btn323</citation>
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670 <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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671 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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672 </citations>
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673 </xml>
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674
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675 </macros>
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