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annotate msconvert_macros.xml @ 13:9337a492ebab draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 73cce4134ad971568ac8e557df97bab93ff24d4d
author galaxyp
date Fri, 25 Apr 2025 10:03:13 +0000
parents 5e94d5403baf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 <macros>
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2 <token name="@VERSION@">3.0.20287</token>
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3 <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
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4 <token name="@PROFILE_VERSION@">23.2</token>
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5 <xml name="msconvertCommand">
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 #import re
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9 #set $ext = $input.ext
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11 ## sanitize display name for use as temp filename
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12 #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier)
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14 #if $ext == 'wiff':
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15 ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
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16 ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
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17 #set inputmask = "'"+$basename+"'"
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18 #elif $ext.endswith('tar'):
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19 ln -s '$input' '${basename}' &&
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20 tar xf '${basename}' &&
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21 #set basename = $os.path.splitext($basename)[0]
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22 #if $ext.startswith('waters'):
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23 #set inputmask = '*.raw'
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24 #elif $ext.startswith('agilent') or $ext.startswith('bruker'):
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25 #set inputmask = '*.d'
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26 #elif $ext.startswith('wiff'):
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27 #set inputmask = '*.wiff *.wiff2'
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28 #else
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29 #raise RuntimeError("Unrecognized type of tar (${ext})")
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30 #end if
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31 #else
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32 ln -s '$input' '${basename}' &&
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33 #set inputmask = "'"+$basename+"'"
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34 #end if
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35
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36 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
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37 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
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38 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
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39 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
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40 #end if
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41
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42 ## CAN_SUDO is "" if successful and "1" otherwise
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43 CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null || echo \$?) &&
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44 echo "CAN SUDO \$CAN_SUDO" &&
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45 if [ -z "\$CAN_SUDO" ]; then
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46 uid=`id -u` &&
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47 gid=`id -g` &&
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48 WINE="wine64_anyuser";
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49 else
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50 WINE="wine64" &&
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51 ## create a writable copy of wine prefix (since copying fails for some html
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52 ## stderr and exit code is swallowed)
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53 export WINEPREFIX=\$(mktemp -d) &&
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54 (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true);
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55 fi
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56 &&
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57 \$WINE msconvert ${inputmask}
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58
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59 --outdir outputs
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60 --${output_type}
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61 $general_options.combineIonMobilitySpectra
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62 $general_options.simAsSpectra
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63 $general_options.srmAsSpectra
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64 $general_options.acceptZeroLengthSpectra
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65 $general_options.ignoreUnknownInstrumentError
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66
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67 #if $general_options.scan_summing.do_scan_summing == "true":
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68 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
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69 #end if
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70
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71 #if $general_options.multi_run_output.do_multi_run_output == "true":
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72 #if len($general_options.multi_run_output.run_index_set) > 0
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73 --runIndexSet "
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74 #for $index in $general_options.multi_run_output.run_index_set
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75 [${index.from},${index.to}]
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76 #end for
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77 "
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78 #end if
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79 #else
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80 --runIndexSet $general_options.multi_run_output.runIndexSet
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81 #end if
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82
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83 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
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84 --stripLocationFromSourceFiles
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85
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86 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
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87 #if $data_processing.peak_picking.pick_peaks == "true"
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88 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
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89 #end if
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90
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91 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
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92 --filter "mzRefiner $input_ident_name
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93 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
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94 thresholdScore=$data_processing.precursor_refinement.thresholdScore
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95 thresholdValue=$data_processing.precursor_refinement.thresholdValue
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96 thresholdStep=$data_processing.precursor_refinement.thresholdStep
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97 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"
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98 #end if
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99
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100 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
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101 --filter "chargeStatePredictor
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102 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
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103 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
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104 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
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105 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
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106 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
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107 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
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108 --filter "turbocharger
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109 minCharge=$data_processing.charge_state_calculation.minCharge
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110 maxCharge=$data_processing.charge_state_calculation.maxCharge
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111 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
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112 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
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113 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
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114 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
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115 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
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116 #end if
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117
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118 #for threshold_entry in $data_processing.thresholds
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119 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
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120 #end for
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121
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122 #if $data_processing.filter_mz_windows.do_mzwindow_filter == "true"
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123 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
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124 #end if
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125
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126 #if $data_processing.etd_filtering.do_etd_filtering == "true"
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127 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
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128 $data_processing.etd_filtering.remove_charge_reduced
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129 $data_processing.etd_filtering.remove_neutral_loss
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130 $data_processing.etd_filtering.blanket_removal
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131 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
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132 #end if
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133
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134 #if $data_processing.ms2denoise.denoise == "true"
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135 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
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136 #end if
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137
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138 #if str($data_processing.ms2deisotope) == "true"
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139 --filter "MS2Deisotope"
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140 #end if
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141
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142 #if $data_processing.demultiplex.demultiplex_on == "true"
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143 --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize"
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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144 #end if
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145
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146 ## SCAN INCLUSION/EXCLUSION FILTERS
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147 #if str($filtering.activation) != "false"
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148 --filter "activation $filtering.activation"
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149 #end if
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150
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151 #if len($filtering.indices) > 0
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152 --filter "index
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153 #for $index in $filtering.indices
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154 [${index.from},${index.to}]
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155 #end for
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156 "
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157 #end if
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158
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159 #if len($filtering.scan_numbers) > 0
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160 --filter "scanNumber
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161 #for $scan_number in $filtering.scan_numbers
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162 [${scan_number.from},${scan_number.to}]
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163 #end for
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164 "
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165 #end if
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166
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167 #if $filtering.strip_it.value
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168 --filter "stripIT"
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169 #end if
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170
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171 #if $filtering.filter_ms_levels.do_ms_level_filter == "true"
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172 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
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173 #end if
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174
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175 #if str($filtering.polarity) != "false"
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176 --filter "polarity $filtering.polarity"
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177 #end if
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178
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179 #if str($filtering.analyzer) != "false"
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180 --filter "analyzer $filtering.analyzer"
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181 #end if
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182
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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183 ## OUTPUT ENCODING
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184 #set $mz_encoding = str($settings.mz_encoding)
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185 #set $intensity_encoding = str($settings.intensity_encoding)
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186 #if $mz_encoding == $intensity_encoding
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187 #if $mz_encoding == "64"
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188 --64
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189 #else
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190 --32
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191 #end if
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192 #else
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193 --mz${mz_encoding}
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194 --inten${intensity_encoding}
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195 #end if
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196
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197 #set binary_compression = str($settings.binary_compression)
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198 #if $binary_compression == "zlib"
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199 --zlib
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200 #else if $binary_compression == "numpressLinearPic"
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201 --numpressLinear --numpressPic
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202 #else if $binary_compression == "numpressLinearSlof"
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203 --numpressLinear --numpressSlof
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204 #else if $binary_compression == "numpressLinear"
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205 --numpressLinear
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206 #else if $binary_compression == "numpressPic"
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207 --numpressPic
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208 #else if $binary_compression == "numpressSlof"
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209 --numpressSlof
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210 #end if
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211
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212 #if $settings.gzip_compression == "true"
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213 --gzip
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214 #end if
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215
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216 #if $general_options.multi_run_output.do_multi_run_output == 'false':
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217 --outfile '${os.path.splitext($basename)[0]}'
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218 #end if
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219 &&
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220 if [ -z "\$CAN_SUDO" ]; then
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221 sudo chown -R \$uid:\$gid './';
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222 fi
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223 #if $general_options.multi_run_output.do_multi_run_output == 'false':
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224 && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
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225 #else
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226 ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
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227 ## this won't be necessay from Galaxy 25.0 https://github.com/galaxyproject/galaxy/pull/19954
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228 #if $output_type == 'mzML' or $output_type == 'mzXML'
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229 && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
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230 ## a newline is needed after `#echo ...` therefore the `;'` on the next line
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231 ;'
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232 #end if
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233 #end if
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234
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235 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
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236 && mv '$output_refinement_name' '$output_refinement';
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237 #end if
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238 ]]>
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239 </command>
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240 </xml>
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241
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242 <xml name="msconvertInputParameters">
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243 <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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244 <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator>
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245 </param>
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246
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247 <param name="output_type" type="select" label="Output Type">
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248 <option value="mz5" selected="true">mz5</option>
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249 <option value="mzML">mzML</option>
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250 <option value="mzXML">mzXML</option>
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251 <option value="mgf">mgf</option>
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252 <option value="ms2">ms2</option>
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253 </param>
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254
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255 <section name="data_processing" title="Data Processing Filters">
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256 <conditional name="peak_picking">
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257 <param type="select" name="pick_peaks" label="Apply peak picking?">
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258 <option value="true">Yes</option>
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259 <option value="false" selected="true">No</option>
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260 </param>
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261 <when value="false" />
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262 <when value="true">
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263 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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264 <option value="1">MS1 Only (1)</option>
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265 <option value="2">MS2 Only (2)</option>
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266 <option value="2-">MS2 and on (2-)</option>
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267 <option value="1-" selected="true">All Levels (1-)</option>
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268 </param>
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269 <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
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270 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
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271 <option value="cwt">CantWaiT - continuous wavelet transform</option>
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272 </param>
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273 </when>
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274 </conditional>
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275
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276 <conditional name="precursor_refinement">
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277 <param type="select" name="use_mzrefinement" label="Apply m/z refinement with identification data?">
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278 <option value="true">Yes</option>
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279 <option value="false" selected="true">No</option>
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280 </param>
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281 <when value="false"></when>
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282 <when value="true">
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283 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
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284 <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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285 <sanitizer>
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286 <valid initial="string.letters" />
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287 </sanitizer>
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288 </param>
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289 <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10.">
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290 <sanitizer>
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291 <valid initial="string.letters,string.digits">
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292 <add value="-" />
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293 </valid>
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294 </sanitizer>
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295 </param>
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296 <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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297 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
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298 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
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299 <option value="1">MS1 Only (1)</option>
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300 <option value="2">MS2 Only (2)</option>
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301 <option value="2-">MS2 and on (2-)</option>
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302 <option value="1-" selected="true">All Levels (1-)</option>
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303 </param>
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304 </when>
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305 </conditional>
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306
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307 <conditional name="charge_state_calculation">
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308 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
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309 <option value="false">no</option>
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310 <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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311 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
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312 </param>
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313 <when value="false" />
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314 <when value="predictor">
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315 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
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316 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
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317 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
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318 <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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319 <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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320 </when>
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321 <when value="turbocharger">
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322 <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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323 <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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324 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
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325 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
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326 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
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327 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
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328 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
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329 </when>
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330 </conditional>
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331
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332 <repeat name="thresholds" title="Filter by Threshold">
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333 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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334 <option value="count">Peak count</option>
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335 <option value="count-after-ties">Peak count (after ties)</option>
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336 <option value="absolute">Peak absolute intensity</option>
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337 <option value="bpi-relative">Fraction of base peak intensity</option>
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338 <option value="tic-relative">Fraction of total ion current</option>
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339 <option value="tic-fraction">Aggregate fraction of total ion current</option>
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340 </param>
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341 <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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342 <param type="select" label="Keep" name="orientation">
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343 <option value="most-intense">Most intense peaks</option>
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344 <option value="least-intense">Least intense peaks</option>
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345 </param>
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346 </repeat>
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347
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348 <conditional name="filter_mz_windows">
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349 <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">
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350 <option value="true">Yes</option>
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351 <option value="false" selected="true">No</option>
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352 </param>
4
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353 <when value="false" />
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354 <when value="true">
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355 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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356 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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357 </when>
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358 </conditional>
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359
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360 <conditional name="etd_filtering">
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361 <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">
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362 <option value="true">Yes</option>
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363 <option value="false" selected="true">No</option>
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364 </param>
4
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365 <when value="false" />
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366 <when value="true">
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367 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
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368 <option value="true" selected="true">yes</option>
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369 <option value="false">no</option>
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370 </param>
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371 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
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372 <option value="true" selected="true">yes</option>
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373 <option value="false">no</option>
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374 </param>
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375 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
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376 <option value="true" selected="true">yes</option>
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377 <option value="false">no</option>
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378 </param>
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379 <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
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380 <option value="true" selected="true">yes</option>
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381 <option value="false">no</option>
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382 </param>
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383 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
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384 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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385 <option value="MZ" selected="true">mz</option>
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386 <option value="PPM">ppm</option>
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387 </param>
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388 </when>
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389 </conditional>
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390
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391 <conditional name="ms2denoise">
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392 <param name="denoise" type="select" label="De-noise MS2 with moving window filter">
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393 <option value="true">Yes</option>
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394 <option value="false" selected="true">No</option>
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395 </param>
4
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396 <when value="true">
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397 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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398 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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399 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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400 </when>
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401 <when value="false" />
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402 </conditional>
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403
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404 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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405
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06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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406 <conditional name="demultiplex">
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407 <param name="demultiplex_on" type="select" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)">
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408 <option value="true">Yes</option>
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409 <option value="false" selected="true">No</option>
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410 </param>
10
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411 <when value="true">
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412 <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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413 <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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414 <option value="MZ">mz</option>
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415 <option value="PPM" selected="true">ppm</option>
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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416 </param>
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417 <param name="nnlsMaxIter" type="integer" label="Maximum iterations for NNLS solve" value="50"/>
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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418 <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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419 <param name="demuxBlockExtra" type="float" label="DemuxBlockExtra" help="Multiplier to expand or reduce the # of spectra considered when demultiplexing. If 0, a fully determined system of equations is built. If > 1.0, the number of rows included in the system is extended DemuxBlockExtra * (# scans in 1 duty cycle)" value="0"/>
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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420 <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
12
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421 <param name="noSumNormalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No sum normalization?" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
10
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422 <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
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423 <option value="none" selected="true">None</option>
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424 <option value="overlap_only">Overlap only</option>
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425 </param>
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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426 <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
12
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427 <param name="noWeighting" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
10
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428 <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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429 </when>
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430 <when value="false" />
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431 </conditional>
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432
4
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433 </section>
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434
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435 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
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436
4
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437 <param name="activation" type="select" label="Filter by Activation">
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438 <option value="false" selected="true">no</option>
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439 <option value="ETD">ETD</option>
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440 <option value="CID">CID</option>
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441 <option value="SA">SA</option>
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442 <option value="HCD">HCD</option>
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443 <option value="BIRD">BIRD</option>
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444 <option value="ECD">ECD</option>
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445 <option value="IRMPD">IRMPD</option>
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446 <option value="PD">PD</option>
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447 <option value="PSD">PSD</option>
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448 <option value="PQD">PQD</option>
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449 <option value="SID">SID</option>
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450 <option value="SORI">SORI</option>
4
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451 </param>
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452
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453 <repeat name="indices" title="Filter Scan Indices">
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454 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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455 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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456 </repeat>
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457
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458 <repeat name="scan_numbers" title="Filter Scan Numbers">
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459 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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460 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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461 </repeat>
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462
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463 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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464
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465 <conditional name="filter_ms_levels">
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466 <param name="do_ms_level_filter" type="select" label="Filter MS Levels">
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467 <option value="true">Yes</option>
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468 <option value="false" selected="true">No</option>
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469 </param>
4
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470 <when value="false" />
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471 <when value="true">
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472 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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473 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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474 </when>
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475 </conditional>
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476
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477 <param name="polarity" type="select" label="Filter by Polarity">
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478 <option value="false" selected="true">no</option>
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479 <option value="positive">positive</option>
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480 <option value="negative">negative</option>
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481 </param>
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482
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483 <param name="analyzer" type="select" label="Filter by Analyzer">
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484 <option value="false" selected="true">no</option>
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485 <option value="quad">Quadrupole</option>
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486 <option value="orbi">Orbitrap</option>
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487 <option value="FT">Fourier-transform</option>
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488 <option value="IT">Ion trap</option>
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489 <option value="TOF">Time of flight</option>
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490 </param>
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491 </section>
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492
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493 <section name="general_options" title="General Options">
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494 <param argument="--combineIonMobilitySpectra" type="boolean" truevalue="--combineIonMobilitySpectra" falsevalue="" 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." />
7
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495
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496 <conditional name="scan_summing">
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497 <param name="do_scan_summing" type="select" 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">
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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498 <option value="true">Yes</option>
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499 <option value="false" selected="true">No</option>
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500 </param>
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501 <when value="false" />
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502 <when value="true">
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diff changeset
503 <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." />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
504 <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." />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
505 <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." />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
506 </when>
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diff changeset
507 </conditional>
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diff changeset
508
10
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diff changeset
509 <param argument="--simAsSpectra" type="boolean" truevalue="--simAsSpectra" falsevalue="" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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diff changeset
510 <param argument="--srmAsSpectra" type="boolean" truevalue="--srmAsSpectra" falsevalue="" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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diff changeset
511 <param argument="--acceptZeroLengthSpectra" type="boolean" truevalue="--acceptZeroLengthSpectra" falsevalue="" 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" />
06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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diff changeset
512 <param argument="--ignoreUnknownInstrumentError" type="boolean" truevalue="--ignoreUnknownInstrumentError" falsevalue="" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" />
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e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
513
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
514 <conditional name="multi_run_output">
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diff changeset
515 <param name="do_multi_run_output" type="select" 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)">
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
516 <option value="true">Yes</option>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
517 <option value="false" selected="true">No</option>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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parents: 11
diff changeset
518 </param>
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
519 <when value="false">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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520 <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)" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
521 </when>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
522 <when value="true">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
523 <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">
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
524 <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
525 <param name="to" type="integer" label="Run Index To" value="0" min="0" optional="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
526 </repeat>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
527 </when>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
528 </conditional>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
529 </section>
4
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parents: 3
diff changeset
530
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
531 <section name="settings" title="Output Encoding Settings">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
532 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
533 <option value="64" selected="true">64</option>
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parents: 3
diff changeset
534 <option value="32">32</option>
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parents: 3
diff changeset
535 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
536 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
537 <option value="64">64</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
538 <option value="32" selected="true">32</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
539 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
540 <param type="select" name="binary_compression" label="Binary data compression">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
541 <option value="false">None</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
542 <option value="zlib" selected="true">zlib</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 3
diff changeset
543 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 3
diff changeset
544 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 3
diff changeset
545 <option value="numpressLinear">numpressLinear only</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 3
diff changeset
546 <option value="numpressPic">numpressPic only</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
547 <option value="numpressSlof">numpressSlof only</option>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
548 </param>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
549 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
550 </section>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
551 </xml>
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06747cba5685 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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552
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158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
553 <xml name="msconvertOutput">
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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554 <outputs>
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e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
555 <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" >
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parents: 11
diff changeset
556 <filter>general_options['multi_run_output']['do_multi_run_output'] == "false"</filter>
4
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
557 <change_format>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
558 <when input="output_type" value="mz5" format="mz5" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents: 3
diff changeset
559 <when input="output_type" value="mzXML" format="mzxml" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
560 <when input="output_type" value="ms2" format="ms2" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
561 <when input="output_type" value="mgf" format="mgf" />
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
562 </change_format>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
diff changeset
563 </data>
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e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
564 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
565 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == "true"</filter>
4
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parents: 3
diff changeset
566 </data>
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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parents: 11
diff changeset
567 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection">
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
568 <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter>
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9337a492ebab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 73cce4134ad971568ac8e557df97bab93ff24d4d
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parents: 12
diff changeset
569 <discover_datasets pattern="__name_and_ext__" directory="outputs" sort_by="designation" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
570 </collection>
4
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diff changeset
571 </outputs>
158a71ee5733 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents: 3
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572 </xml>
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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parents: 5
diff changeset
573
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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parents: 5
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574
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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parents: 5
diff changeset
575 <xml name="msconvert_tests">
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
576 <test expect_num_outputs="1">
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
577 <param name="input" value="small.RAW" ftype="thermo.raw" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
578 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
579 <param name="output_type" value="mzML" />
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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parents: 11
diff changeset
580 <param name="data_processing|peak_picking|pick_peaks" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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parents: 11
diff changeset
581 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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parents: 11
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582 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" />
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052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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diff changeset
583 <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
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e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
584 </test>
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diff changeset
585 <test expect_num_outputs="1">
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052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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parents: 10
diff changeset
586 <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
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e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 6
diff changeset
587 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
588 <param name="output_type" value="mzML" />
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
589 <param name="general_options|combineIonMobilitySpectra" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
590 <param name="general_options|scan_summing|do_scan_summing" value="true" />
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052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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diff changeset
591 <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
592 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
593 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
594 <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
595 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
596 <param name="output_type" value="mzML" />
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
597 <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
598 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
599 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
600 <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
601 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
602 <param name="output_type" value="mzXML" />
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
603 <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
604 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
605 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
606 <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
607 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
608 <param name="output_type" value="mzML" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
609 <param name="data_processing|peak_picking|pick_peaks" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
610 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
611 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" />
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
612 <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
613 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
614 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
615 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
616 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
617 <param name="output_type" value="mzXML" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
618 <param name="general_options|multi_run_output|do_multi_run_output" value="false" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
619 <param name="general_options|multi_run_output|runIndexSet" value="1" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
620 <param name="filtering|indices_0|from" value="0" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
621 <param name="filtering|indices_0|to" value="499" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
622 <param name="general_options|srmAsSpectra" value="true" />
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
623 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
624 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
625 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
626 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
627 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
628 <param name="output_type" value="mzML" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
629 <param name="general_options|multi_run_output|do_multi_run_output" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
630 <param name="general_options|multi_run_output|run_index_set_0|from" value="0" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
631 <param name="general_options|multi_run_output|run_index_set_0|to" value="1" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
632 <output_collection name="multi_run_output_list" type="list">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
633 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
634 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
635 </output_collection>
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
636 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
637 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
638 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
639 <param name="license_agreement" value="true" />
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
640 <param name="output_type" value="mzML" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
641 <param name="general_options|multi_run_output|do_multi_run_output" value="true" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
642 <output_collection name="multi_run_output_list" type="list">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
643 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
644 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
645 </output_collection>
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
646 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
647
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
648 <!-- this data file only has profile MS1, so the result is the same -->
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
649 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
650 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
651 <param name="license_agreement" value="true" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
652 <param name="output_type" value="mz5" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
653 <param name="settings|mz_encoding" value="64" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
654 <param name="settings|intensity_encoding" value="64" />
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
655 <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
656 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
657 <!-- TODO: how to test gzipped output?
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
658 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
659 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
660 <param name="output_type" value="mzXML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
661 <param name="mz_encoding" value="32" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
662 <param name="intensity_encoding" value="32" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
663 <param name="settings|binary_compression" value="false" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
664 <param name="gzip_compression" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
665 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
666 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
667 <test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
668 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
669 <param name="output_type" value="mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
670 <param name="mz_encoding" value="32" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
671 <param name="intensity_encoding" value="32" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
672 <param name="settings|binary_compression" value="false" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
673 <param name="gzip_compression" value="true" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
674 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
675 </test>-->
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
676 <test expect_num_outputs="2">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
677 <param name="input" value="Rpal_01.mz5" ftype="mz5" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
678 <param name="license_agreement" value="true" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
679 <param name="output_type" value="mzML" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
680 <param name="settings|binary_compression" value="numpressLinearPic" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
681 <param name="data_processing|precursor_refinement|use_mzrefinement" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
682 <param name="data_processing|precursor_refinement|input_ident" value="Rpal_01.pepXML" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
683 <param name="data_processing|precursor_refinement|thresholdScore" value="mvh" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
684 <param name="data_processing|precursor_refinement|thresholdValue" value="40-" />
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
685 <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" />
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
686 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
687 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
688 <test expect_num_outputs="1">
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
689 <param name="input" value="small.mzML" ftype="mzml" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
690 <param name="license_agreement" value="true" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
691 <param name="output_type" value="mzML" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
692
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
693 <param name="data_processing|peak_picking|pick_peaks" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
694 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="cwt" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
695 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
696
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
697 <param name="data_processing|thresholds_0|threshold_type" value="count" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
698 <param name="data_processing|thresholds_0|value" value="100" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
699 <param name="data_processing|thresholds_0|orientation" value="most-intense" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
700 <param name="data_processing|thresholds_1|threshold_type" value="absolute" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
701 <param name="data_processing|thresholds_1|value" value="1" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
702 <param name="data_processing|thresholds_1|orientation" value="most-intense" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
703
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
704 <param name="data_processing|filter_mz_windows|do_mzwindow_filter" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
705 <param name="data_processing|filter_mz_windows|mz_window_from" value="420" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
706 <param name="data_processing|filter_mz_windows|mz_window_to" value="840" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
707
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
708 <param name="filtering|indices_0|from" value="0" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
709 <param name="filtering|indices_0|to" value="20" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
710 <param name="filtering|indices_1|from" value="41" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
711 <param name="filtering|indices_1|to" value="41" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
712
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
713 <param name="filtering|filter_ms_levels|do_ms_level_filter" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
714 <param name="filtering|filter_ms_levels|ms_level_from" value="2" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
715 <param name="filtering|filter_ms_levels|ms_level_to" value="2" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
716
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
717 <param name="filtering|scan_numbers_0|from" value="5" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
718 <param name="filtering|scan_numbers_0|to" value="25" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
719 <param name="filtering|scan_numbers_1|from" value="40" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
720 <param name="filtering|scan_numbers_1|to" value="40" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
721
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
722 <param name="data_processing|ms2deisotope" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
723
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
724 <param name="data_processing|ms2denoise|denoise" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
725 <param name="data_processing|ms2denoise|num_peaks" value="10" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
726 <param name="data_processing|ms2denoise|window_width" value="40" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
727 <param name="data_processing|ms2denoise|relax" value="false" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
728
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
729 <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="predictor" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
730 <param name="data_processing|charge_state_calculation|predictor_overrideExistingCharge" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
731 <param name="data_processing|charge_state_calculation|minMultipleCharge" value="2" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
732 <param name="data_processing|charge_state_calculation|maxMultipleCharge" value="5" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
733 <param name="data_processing|charge_state_calculation|singleChargeFractionTIC" value="0.95" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
734 <param name="data_processing|charge_state_calculation|maxKnownCharge" value="8" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
735
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
736 <param name="settings|mz_encoding" value="32" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
737 <param name="settings|intensity_encoding" value="32" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
738
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
739 <param name="settings|binary_compression" value="numpressLinearPic" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
740 <output name="output" file="small-composite-test.mzML" ftype="mzml" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
741 </test>
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
742 <test expect_num_outputs="1">
11
052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 10
diff changeset
743 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 6
diff changeset
744 <param name="license_agreement" value="true" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
745 <param name="output_type" value="mzML" />
12
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
746 <param name="settings|binary_compression" value="numpressLinearPic" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
747 <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="turbocharger" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
748 <param name="data_processing|charge_state_calculation|minCharge" value="1" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
749 <param name="data_processing|charge_state_calculation|maxCharge" value="5" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
750 <param name="data_processing|charge_state_calculation|precursorsBefore" value="1" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
751 <param name="data_processing|charge_state_calculation|precursorsAfter" value="1" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
752 <param name="data_processing|charge_state_calculation|halfIsoWidth" value="1.5" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
753 <param name="data_processing|charge_state_calculation|defaultMinCharge" value="1" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
754 <param name="data_processing|charge_state_calculation|defaultMaxCharge" value="5" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
755 <param name="filtering|strip_it" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 11
diff changeset
756 <output name="output" file="small-composite-test-2.mzML" ftype="mzml" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 5
diff changeset
757 </test>
12
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758 <test expect_num_outputs="1">
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759 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
7
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760 <param name="license_agreement" value="true" />
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761 <param name="output_type" value="mzML" />
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diff changeset
762 <param name="filtering|activation" value="CID" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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763 <param name="settings|binary_compression" value="numpressLinearPic" />
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764 <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
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6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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765 </test>
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diff changeset
766 <test expect_num_outputs="1">
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052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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767 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
768 <param name="license_agreement" value="true" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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769 <param name="output_type" value="mzML" />
12
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770 <param name="filtering|polarity" value="positive" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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771 <param name="settings|binary_compression" value="numpressLinearPic" />
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052798dd73dd "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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772 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
6
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773 </test>
12
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diff changeset
774 <test expect_num_outputs="1">
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
775 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
7
e638f7fad66a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
776 <param name="license_agreement" value="true" />
6
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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diff changeset
777 <param name="output_type" value="mzML" />
12
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778 <param name="data_processing|etd_filtering|do_etd_filtering" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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779 <param name="data_processing|etd_filtering|remove_precursor" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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780 <param name="data_processing|etd_filtering|remove_charge_reduced" value="true" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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diff changeset
781 <param name="data_processing|etd_filtering|remove_neutral_loss" value="false" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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782 <param name="data_processing|etd_filtering|blanket_removal" value="false" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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783 <param name="data_processing|etd_filtering|matching_tolerance" value="50" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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784 <param name="data_processing|etd_filtering|matching_tolerance_units" value="PPM" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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785 <param name="settings|binary_compression" value="numpressLinearPic" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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786 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
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diff changeset
787 </test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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788 <!--<test>
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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789 <param name="input" value="small.mzML" />
6b6bba73eadb planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
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790 <param name="output_type" value="mzML" />
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diff changeset
791 <param name="settings|binary_compression" value="numpressLinearPic" />
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792 <output name="output" file="small-deisotope-poisson.mzML" />
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793 </test>-->
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794 </xml>
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795 <xml name="citations">
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796 <citations>
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797 <citation type="doi">10.1093/bioinformatics/btn323</citation>
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798 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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799 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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800 </citations>
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801 </xml>
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802
4
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803 </macros>