Mercurial > repos > galaxyp > msconvert

annotate msconvert_macros.xml.orig @ 10:9d5de24e6ef7 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author galaxyp
date Sat, 23 Feb 2019 06:25:48 -0500
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9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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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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4
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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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10
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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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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 #elif $ext.endswith('tar'):
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18 ln -s '$input' '${basename}' &&
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19 tar xf '${basename}' &&
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20 #set basename = $os.path.splitext($basename)[0]
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21 #else
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22 ln -s '$input' '${basename}' &&
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23 #end if
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24
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25 #if $data_processing.precursor_refinement.use_mzrefinement
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26 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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27 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
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28 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
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29 #end if
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31 uid=`id -u` &&
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32 gid=`id -g` &&
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33
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34 wine64_anyuser msconvert '${basename}'
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35 --outdir outputs
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36 --${output_type}
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37
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38 #if $general_options.combineIonMobilitySpectra:
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39 --combineIonMobilitySpectra
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40 #end if
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41
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42 #if $general_options.simAsSpectra:
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43 --simAsSpectra
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44 #end if
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45
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46 #if $general_options.srmAsSpectra:
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47 --srmAsSpectra
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48 #end if
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49
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50 #if $general_options.acceptZeroLengthSpectra:
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51 --acceptZeroLengthSpectra
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52 #end if
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53
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54 #if $general_options.ignoreUnknownInstrumentError:
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55 --ignoreUnknownInstrumentError
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56 #end if
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57
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58 #if $general_options.scan_summing.do_scan_summing:
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59 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
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60 #end if
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61
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62 #if $general_options.multi_run_output.do_multi_run_output:
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63 #if len($general_options.multi_run_output.run_index_set) > 0
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64 --runIndexSet "
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65 #for $index in $general_options.multi_run_output.run_index_set
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66 [${index.from},${index.to}]
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67 #end for
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68 "
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69 #end if
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70 #else
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71 --runIndexSet $general_options.multi_run_output.runIndexSet
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72 #end if
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73
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74 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
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75 --stripLocationFromSourceFiles
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76
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77 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
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78 #if $data_processing.peak_picking.pick_peaks
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79 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
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80 #end if
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81
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82 #if $data_processing.precursor_refinement.use_mzrefinement
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83 --filter "mzRefiner $input_ident_name
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84 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
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85 thresholdScore=$data_processing.precursor_refinement.thresholdScore
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86 thresholdValue=$data_processing.precursor_refinement.thresholdValue
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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87 thresholdStep=$data_processing.precursor_refinement.thresholdStep
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88 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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89 #end if
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90
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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91 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
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92 --filter "chargeStatePredictor
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93 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
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94 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
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95 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
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96 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
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97 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
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98 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
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99 --filter "turbocharger
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100 minCharge=$data_processing.charge_state_calculation.minCharge
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101 maxCharge=$data_processing.charge_state_calculation.maxCharge
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102 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
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103 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
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104 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
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105 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
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106 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
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107 #end if
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108
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109 #for threshold_entry in $data_processing.thresholds
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110 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
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111 #end for
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112
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113 #if $data_processing.filter_mz_windows.do_mzwindow_filter
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114 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
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115 #end if
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116
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117 #if $data_processing.etd_filtering.do_etd_filtering
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118 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
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119 $data_processing.etd_filtering.remove_charge_reduced
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120 $data_processing.etd_filtering.remove_neutral_loss
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121 $data_processing.etd_filtering.blanket_removal
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122 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
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123 #end if
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124
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125 #if $data_processing.ms2denoise.denoise
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126 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
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127 #end if
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128
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129 #if str($data_processing.ms2deisotope) == "true"
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130 --filter "MS2Deisotope"
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131 #end if
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132
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133
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134 ## SCAN INCLUSION/EXCLUSION FILTERS
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135 #if str($filtering.activation) != "false"
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136 --filter "activation $filtering.activation"
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137 #end if
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138
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139 #if len($filtering.indices) > 0
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140 --filter "index
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141 #for $index in $filtering.indices
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142 [${index.from},${index.to}]
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143 #end for
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144 "
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145 #end if
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146
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147 #if len($filtering.scan_numbers) > 0
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148 --filter "scanNumber
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149 #for $scan_number in $filtering.scan_numbers
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150 [${scan_number.from},${scan_number.to}]
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151 #end for
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152 "
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153 #end if
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154
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155 #if $filtering.strip_it.value
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156 --filter "stripIT"
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157 #end if
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158
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159 #if $filtering.filter_ms_levels.do_ms_level_filter
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160 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
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161 #end if
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162
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163 #if str($filtering.polarity) != "false"
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164 --filter "polarity $filtering.polarity"
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165 #end if
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166
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167 #if str($filtering.analyzer) != "false"
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168 --filter "analyzer $filtering.analyzer"
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169 #end if
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170
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171 ## OUTPUT ENCODING
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172 #set $mz_encoding = str($settings.mz_encoding)
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173 #set $intensity_encoding = str($settings.intensity_encoding)
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174 #if $mz_encoding == $intensity_encoding
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175 #if $mz_encoding == "64"
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176 --64
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177 #else
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178 --32
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179 #end if
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180 #else
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181 --mz${mz_encoding}
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182 --inten${intensity_encoding}
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183 #end if
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184
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185 #set binary_compression = str($settings.binary_compression)
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186 #if $binary_compression == "zlib"
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187 --zlib
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188 #else if $binary_compression == "numpressLinearPic"
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189 --numpressLinear --numpressPic
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190 #else if $binary_compression == "numpressLinearSlof"
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191 --numpressLinear --numpressSlof
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192 #else if $binary_compression == "numpressLinear"
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193 --numpressLinear
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194 #else if $binary_compression == "numpressPic"
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195 --numpressPic
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196 #else if $binary_compression == "numpressSlof"
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197 --numpressSlof
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198 #end if
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199
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200 #if $settings.gzip_compression
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201 --gzip
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202 #end if
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203
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204 #if $general_options.multi_run_output.do_multi_run_output == 'false':
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205 --outfile '${os.path.splitext($basename)[0]}'
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206 && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}'
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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207 #else
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208 && sudo chown \$uid:\$gid 'outputs'/*
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209 && ls -la outputs/
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210 #end if
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211
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212 #if $data_processing.precursor_refinement.use_mzrefinement
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213 && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement'
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214 #end if
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215 ]]>
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216 </command>
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217 </xml>
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218
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219 <xml name="msconvertInputParameters">
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220 <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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221 <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator>
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222 </param>
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223
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224 <param name="output_type" type="select" label="Output Type">
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225 <<<<<<< HEAD
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226 <option value="mz5" selected="true">mz5</option>
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227 <option value="mzml">mzML</option>
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228 <option value="mzxml">mzXML</option>
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229 <option value="mgf">mgf</option>
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230 <option value="ms2">ms2</option>
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231 =======
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232 <option value="mz5" selected="true">mz5</option>
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233 <option value="mzML">mzML</option>
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234 <option value="mzXML">mzXML</option>
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235 <option value="mgf">mgf</option>
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236 <option value="ms2">ms2</option>
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237 >>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213
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238 </param>
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239
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240 <section name="data_processing" title="Data Processing Filters">
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241 <conditional name="peak_picking">
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242 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
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243 <when value="false" />
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244 <when value="true">
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245 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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246 <option value="1">MS1 Only (1)</option>
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247 <option value="2">MS2 Only (2)</option>
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248 <option value="2-">MS2 and on (2-)</option>
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249 <option value="1-" selected="true">All Levels (1-)</option>
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250 </param>
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251 <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)">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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252 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
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253 <option value="cwt">CantWaiT - continuous wavelet transform</option>
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254 </param>
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255 </when>
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256 </conditional>
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257
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258 <conditional name="precursor_refinement">
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259 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
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260 <when value="false"></when>
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261 <when value="true">
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262 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
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263 <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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264 <sanitizer>
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265 <valid initial="string.letters" />
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266 </sanitizer>
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267 </param>
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268 <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.">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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269 <sanitizer>
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270 <valid initial="string.letters,string.digits">
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271 <add value="-" />
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272 </valid>
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273 </sanitizer>
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274 </param>
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275 <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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276 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
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277 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
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278 <option value="1">MS1 Only (1)</option>
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279 <option value="2">MS2 Only (2)</option>
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280 <option value="2-">MS2 and on (2-)</option>
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281 <option value="1-" selected="true">All Levels (1-)</option>
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282 </param>
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283 </when>
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284 </conditional>
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285
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286 <conditional name="charge_state_calculation">
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287 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
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288 <option value="false">no</option>
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289 <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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290 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
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291 </param>
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292 <when value="false" />
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293 <when value="predictor">
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294 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
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295 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
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296 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
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297 <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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298 <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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299 </when>
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300 <when value="turbocharger">
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301 <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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302 <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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303 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
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304 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
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305 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
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306 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
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307 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
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308 </when>
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309 </conditional>
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310
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311 <repeat name="thresholds" title="Filter by Threshold">
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312 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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313 <option value="count">Peak count</option>
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314 <option value="count-after-ties">Peak count (after ties)</option>
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315 <option value="absolute">Peak absolute intensity</option>
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316 <option value="bpi-relative">Fraction of base peak intensity</option>
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317 <option value="tic-relative">Fraction of total ion current</option>
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318 <option value="tic-fraction">Aggregate fraction of total ion current</option>
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319 </param>
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320 <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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321 <param type="select" label="Keep" name="orientation">
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322 <option value="most-intense">Most intense peaks</option>
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323 <option value="least-intense">Least intense peaks</option>
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324 </param>
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325 </repeat>
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326
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327 <conditional name="filter_mz_windows">
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328 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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329 <when value="false" />
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330 <when value="true">
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331 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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332 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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333 </when>
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334 </conditional>
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335
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336 <conditional name="etd_filtering">
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337 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
338 <when value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
339 <when value="true">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
340 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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341 <option value="true" selected="true">yes</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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342 <option value="false">no</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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343 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
344 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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345 <option value="true" selected="true">yes</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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346 <option value="false">no</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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347 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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348 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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349 <option value="true" selected="true">yes</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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350 <option value="false">no</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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351 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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352 <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)">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
353 <option value="true" selected="true">yes</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
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354 <option value="false">no</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
355 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
356 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
357 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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358 <option value="MZ" selected="true">mz</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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359 <option value="PPM">ppm</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
360 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
361 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
362 </conditional>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
363
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
364 <conditional name="ms2denoise">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
365 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
366 <when value="true">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
367 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
368 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
369 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
370 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
371 <when value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
372 </conditional>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
373
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
374 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
375
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
376 </section>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
377
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
378
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
379 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
380
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
381 <param name="activation" type="select" label="Filter by Activation">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
382 <option value="false" selected="true">no</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
383 <option value="ETD">ETD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
384 <option value="CID">CID</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
385 <option value="SA">SA</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
386 <option value="HCD">HCD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
387 <option value="BIRD">BIRD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
388 <option value="ECD">ECD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
389 <option value="IRMPD">IRMPD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
390 <option value="PD">PD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
391 <option value="PSD">PSD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
392 <option value="PQD">PQD</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
393 <option value="SID">SID</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
394 <option value="SORI">SORI</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
395 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
396
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
397 <repeat name="indices" title="Filter Scan Indices">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
398 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
399 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
400 </repeat>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
401
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
402 <repeat name="scan_numbers" title="Filter Scan Numbers">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
403 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
404 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
405 </repeat>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
406
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
407 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
408
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
409 <conditional name="filter_ms_levels">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
410 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
411 <when value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
412 <when value="true">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
413 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
414 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
415 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
416 </conditional>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
417
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
418 <param name="polarity" type="select" label="Filter by Polarity">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
419 <option value="false" selected="true">no</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
420 <option value="positive">positive</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
421 <option value="negative">negative</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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422 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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423
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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424 <param name="analyzer" type="select" label="Filter by Analyzer">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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425 <option value="false" selected="true">no</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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426 <option value="quad">Quadrupole</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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427 <option value="orbi">Orbitrap</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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428 <option value="FT">Fourier-transform</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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429 <option value="IT">Ion trap</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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430 <option value="TOF">Time of flight</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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431 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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432 </section>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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433
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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434 <section name="general_options" title="General Options">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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435 <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." />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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436
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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437 <conditional name="scan_summing">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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438 <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" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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439 <when value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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440 <when value="true">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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441 <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." />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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442 <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." />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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443 <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." />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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444 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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445 </conditional>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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446
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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447 <param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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448 <param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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449 <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" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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450 <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" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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451
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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452 <conditional name="multi_run_output">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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453 <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)" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
454 <when value="false">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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455 <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)" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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456 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
457 <when value="true">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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458 <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">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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459 <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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460 <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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461 </repeat>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
462 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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463 </conditional>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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464 </section>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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465
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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466 <section name="settings" title="Output Encoding Settings">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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467 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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468 <option value="64" selected="true">64</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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469 <option value="32">32</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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470 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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471 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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472 <option value="64">64</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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473 <option value="32" selected="true">32</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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474 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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475 <param type="select" name="binary_compression" label="Binary data compression">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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476 <option value="false">None</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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477 <option value="zlib" selected="true">zlib</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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478 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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479 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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480 <option value="numpressLinear">numpressLinear only</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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481 <option value="numpressPic">numpressPic only</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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482 <option value="numpressSlof">numpressSlof only</option>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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483 </param>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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484 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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485 </section>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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486 </xml>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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487
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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488 <xml name="msconvertOutput">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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489 <outputs>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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490 <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
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491 <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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492 <change_format>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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493 <when input="output_type" value="mz5" format="mz5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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494 <when input="output_type" value="mzxml" format="mzxml" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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495 <when input="output_type" value="ms2" format="ms2" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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496 <when input="output_type" value="mgf" format="mgf" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
497 </change_format>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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498 </data>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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499 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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500 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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501 </data>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents:
diff changeset
502 <collection name="multi_run_output_list" type="list" label="${($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:
diff changeset
503 <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:
diff changeset
504 <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:
diff changeset
505 </collection>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
506 </outputs>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
507 </xml>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
508
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
509
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
510 <xml name="msconvert_tests">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
511 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
512 <param name="input" value="small.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
513 <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:
diff changeset
514 <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:
diff changeset
515 <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:
diff changeset
516 <param name="pick_peaks_algorithm" value="cwt" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
517 <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:
diff changeset
518 <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:
diff changeset
519 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
520 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
521 <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:
diff changeset
522 <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:
diff changeset
523 <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:
diff changeset
524 <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:
diff changeset
525 <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:
diff changeset
526 <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:
diff changeset
527 <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:
diff changeset
528 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
529 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
530 <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:
diff changeset
531 <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:
diff changeset
532 <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:
diff changeset
533 <param name="combineIonMobilitySpectra" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
534 <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:
diff changeset
535 <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:
diff changeset
536 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
537 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
538 <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:
diff changeset
539 <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:
diff changeset
540 <<<<<<< HEAD
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
541 <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:
diff changeset
542 <output name="output" file="MassLynxTest.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
543 =======
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
544 <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:
diff changeset
545 <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:
diff changeset
546 >>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
547 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
548 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
549 <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:
diff changeset
550 <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:
diff changeset
551 <<<<<<< HEAD
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
552 <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:
diff changeset
553 <output name="output" file="AgilentMassHunterTest.mzXML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
554 =======
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
555 <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:
diff changeset
556 <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:
diff changeset
557 >>>>>>> 4d10e7e3d0c5541f26c6de354471c71aa0e61213
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
558 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
559 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
560 <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:
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:
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:
diff changeset
563 <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:
diff changeset
564 <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:
diff changeset
565 <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:
diff changeset
566 <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:
diff changeset
567 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
568 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
569 <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:
diff changeset
570 <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:
diff changeset
571 <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:
diff changeset
572 <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:
diff changeset
573 <param name="runIndexSet" value="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
574 <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:
diff changeset
575 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
576 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
577 <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:
diff changeset
578 <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:
diff changeset
579 <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:
diff changeset
580 <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:
diff changeset
581 <param name="runIndexSet" value="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
582 <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:
diff changeset
583 <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:
diff changeset
584 <param name="srmAsSpectra" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
585 <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:
diff changeset
586 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
587 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
588 <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:
diff changeset
589 <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:
diff changeset
590 <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:
diff changeset
591 <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:
diff changeset
592 <param name="runIndexSet" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
593 <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:
diff changeset
594 <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:
diff changeset
595 <param name="srmAsSpectra" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
596 <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:
diff changeset
597 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
598 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
599 <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:
diff changeset
600 <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:
diff changeset
601 <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:
diff changeset
602 <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:
diff changeset
603 <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:
diff changeset
604 <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:
diff changeset
605 <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:
diff changeset
606 <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:
diff changeset
607 <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:
diff changeset
608 </output_collection>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
609 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
610 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
611 <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:
diff changeset
612 <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:
diff changeset
613 <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:
diff changeset
614 <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:
diff changeset
615 <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:
diff changeset
616 <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:
diff changeset
617 <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:
diff changeset
618 </output_collection>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
619 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
620
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
621 <!-- this data file only has profile MS1, so the result is the same -->
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
622 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
623 <param name="input" value="small.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
624 <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:
diff changeset
625 <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:
diff changeset
626 <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:
diff changeset
627 <param name="pick_peaks_algorithm" value="cwt" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
628 <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:
diff changeset
629 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="6" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
630 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
631 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
632 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
633 <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:
diff changeset
634 <param name="output_type" value="mz5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
635 <param name="mz_encoding" value="64" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
636 <param name="intensity_encoding" value="64" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
637 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
638 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
639 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
640 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
641 <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:
diff changeset
642 <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:
diff changeset
643 <param name="mz_encoding" value="32" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
644 <param name="intensity_encoding" value="32" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
645 <output name="output" file="small-zlib-32.mzXML" lines_diff="6" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
646 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
647 <!-- TODO: how to test gzipped output?
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
648 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
649 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
650 <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:
diff changeset
651 <param name="mz_encoding" value="32" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
652 <param name="intensity_encoding" value="32" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
653 <param name="binary_compression" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
654 <param name="gzip_compression" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
655 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
656 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
657 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
658 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
659 <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:
diff changeset
660 <param name="mz_encoding" value="32" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
661 <param name="intensity_encoding" value="32" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
662 <param name="binary_compression" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
663 <param name="gzip_compression" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
664 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
665 </test>-->
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
666
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
667 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
668 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
669 <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:
diff changeset
670 <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:
diff changeset
671 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
672 <output name="output" file="small-numpressLP.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
673 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
674
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
675 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
676 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
677 <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:
diff changeset
678 <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:
diff changeset
679 <param name="binary_compression" value="numpressLinearSlof" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
680 <output name="output" file="small-numpressLS.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
681 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
682
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
683 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
684 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
685 <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:
diff changeset
686 <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:
diff changeset
687 <param name="binary_compression" value="numpressLinear" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
688 <output name="output" file="small-numpressL.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
689 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
690
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
691 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
692 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
693 <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:
diff changeset
694 <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:
diff changeset
695 <param name="binary_compression" value="numpressPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
696 <output name="output" file="small-numpressP.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
697 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
698
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
699 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
700 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
701 <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:
diff changeset
702 <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:
diff changeset
703 <param name="binary_compression" value="numpressSlof" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
704 <output name="output" file="small-numpressS.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
705 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
706
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
707 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
708 <param name="input" value="Rpal_01.mz5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
709 <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:
diff changeset
710 <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:
diff changeset
711 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
712 <param name="use_mzrefinement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
713 <param name="input_ident" value="Rpal_01.pepXML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
714 <param name="thresholdScore" value="mvh" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
715 <param name="thresholdValue" value="40-" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
716 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
717 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
718 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
719
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
720 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
721 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
722 <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:
diff changeset
723 <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:
diff changeset
724 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
725 <param name="charge_state_calculation_method" value="predictor" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
726 <param name="predictor_overrideExistingCharge" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
727 <param name="minMultipleCharge" value="2" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
728 <param name="maxMultipleCharge" value="5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
729 <param name="singleChargeFractionTIC" value="0.95" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
730 <param name="maxKnownCharge" value="8" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
731 <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
732 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
733 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
734 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
735 <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:
diff changeset
736 <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:
diff changeset
737 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
738 <param name="charge_state_calculation_method" value="turbocharger" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
739 <param name="minCharge" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
740 <param name="maxCharge" value="5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
741 <param name="precursorsBefore" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
742 <param name="precursorsAfter" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
743 <param name="halfIsoWidth" value="1.5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
744 <param name="defaultMinCharge" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
745 <param name="defaultMaxCharge" value="5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
746 <output name="output" file="small-turbocharger.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
747 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
748 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
749 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
750 <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:
diff changeset
751 <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:
diff changeset
752 <param name="do_etd_filtering" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
753 <param name="remove_precursor" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
754 <param name="remove_charge_reduced" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
755 <param name="remove_neutral_loss" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
756 <param name="blanket_removal" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
757 <param name="matching_tolerance" value="50" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
758 <param name="matching_tolerance_units" value="ppm" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
759 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
760 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
761 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
762 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
763 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
764 <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:
diff changeset
765 <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:
diff changeset
766 <param name="thresholds_0|threshold_type" value="count" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
767 <param name="thresholds_0|value" value="100" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
768 <param name="thresholds_0|orientation" value="most-intense" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
769 <param name="thresholds_1|threshold_type" value="absolute" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
770 <param name="thresholds_1|value" value="1" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
771 <param name="thresholds_1|orientation" value="most-intense" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
772 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
773 <output name="output" file="small-threshold.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
774 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
775 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
776 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
777 <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:
diff changeset
778 <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:
diff changeset
779 <param name="do_mzwindow_filter" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
780 <param name="mz_window_from" value="420" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
781 <param name="mz_window_to" value="840" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
782 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
783 <output name="output" file="small-mzWindow.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
784 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
785 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
786 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
787 <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:
diff changeset
788 <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:
diff changeset
789 <param name="denoise" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
790 <param name="num_peaks" value="10" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
791 <param name="window_width" value="40" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
792 <param name="relax" value="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
793 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
794 <output name="output" file="small-denoise.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
795 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
796 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
797 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
798 <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:
diff changeset
799 <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:
diff changeset
800 <param name="ms2deisotope" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
801 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
802 <output name="output" file="small-deisotope.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
803 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
804 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
805 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
806 <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:
diff changeset
807 <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:
diff changeset
808 <param name="activation" value="CID" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
809 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
810 <output name="output" file="small-activation.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
811 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
812 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
813 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
814 <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:
diff changeset
815 <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:
diff changeset
816 <param name="indices_0|from" value="2" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
817 <param name="indices_0|to" value="4" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
818 <param name="indices_1|from" value="10" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
819 <param name="indices_1|to" value="10" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
820 <param name="indices_2|from" value="13" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
821 <param name="indices_2|to" value="15" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
822 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
823 <output name="output" file="small-index-filter.mzML" lines_diff="32" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
824 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
825 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
826 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
827 <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:
diff changeset
828 <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:
diff changeset
829 <param name="strip_it" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
830 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
831 <output name="output" file="small-strip-it.mzML" lines_diff="100" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
832 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
833 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
834 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
835 <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:
diff changeset
836 <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:
diff changeset
837 <param name="do_ms_level_filter" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
838 <param name="ms_level_from" value="2" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
839 <param name="ms_level_to" value="2" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
840 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
841 <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
842 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
843 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
844 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
845 <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:
diff changeset
846 <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:
diff changeset
847 <param name="polarity" value="positive" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
848 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
849 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
850 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
851 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
852 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
853 <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:
diff changeset
854 <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:
diff changeset
855 <param name="analyzer" value="IT" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
856 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
857 <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
858 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
859 <test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
860 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
861 <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:
diff changeset
862 <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:
diff changeset
863 <param name="scan_numbers_0|from" value="3" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
864 <param name="scan_numbers_0|to" value="5" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
865 <param name="scan_numbers_1|from" value="11" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
866 <param name="scan_numbers_1|to" value="11" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
867 <param name="scan_numbers_2|from" value="14" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
868 <param name="scan_numbers_2|to" value="16" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
869 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
870 <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above -->
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
871 </test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
872 <!--<test>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
873 <param name="input" value="small.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
874 <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:
diff changeset
875 <param name="binary_compression" value="numpressLinearPic" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
876 <output name="output" file="small-deisotope-poisson.mzML" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
877 </test>-->
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
878 </xml>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
879 <xml name="msconvert_help">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
880 **What it does**
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
881
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
882 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.
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
883
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
884 You can view the original documentation here_.
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
885
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
886 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
887 </xml>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
888
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents:
diff changeset
889 <xml name="citations">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
890 <citations>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
891 <citation type="doi">10.1093/bioinformatics/btn323</citation>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
892 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
893 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
894 </citations>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
895 </xml>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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896
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
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diff changeset
897 </macros>