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annotate msconvert_macros.xml @ 18:331a50e8fd2f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
author galaxyp
date Mon, 10 Mar 2025 07:48:32 +0000
parents ab6c14374bc0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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1 <macros>
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2 <token name="@VERSION@">3.0.20287</token>
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
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3 <token name="@FULL_VERSION@">@VERSION@-769529fa4</token>
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4 <token name="@PROFILE_VERSION@">24.2</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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13
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14 #if $ext == 'wiff':
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15 ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
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16 ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
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17 #set inputmask = "'"+$basename+"'"
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18 #elif $ext.endswith('tar'):
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19 ln -s '$input' '${basename}' &&
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20 tar xf '${basename}' &&
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21 #set basename = $os.path.splitext($basename)[0]
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22 #if $ext.startswith('waters'):
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23 #set inputmask = '*.raw'
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24 #elif $ext.startswith('agilent') or $ext.startswith('bruker'):
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25 #set inputmask = '*.d'
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26 #elif $ext.startswith('wiff'):
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27 #set inputmask = '*.wiff *.wiff2'
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28 #else
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29 #raise RuntimeError("Unrecognized type of tar (${ext})")
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30 #end if
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31 #else
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32 ln -s '$input' '${basename}' &&
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33 #set inputmask = "'"+$basename+"'"
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34 #end if
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35
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36 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
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37 #set input_ident_name = ".".join((os.path.splitext($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=\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) &&
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43 if [ "\$CAN_SUDO" -eq "0" ]; then
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44 uid=`id -u` &&
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45 gid=`id -g` &&
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46 WINE="wine64_anyuser";
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47 else
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48 WINE="wine64" &&
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49 ## create a writable copy of wine prefix (since copying fails for some html
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50 ## stderr and exit code is swallowed)
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51 export WINEPREFIX=\$(mktemp -d) &&
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52 (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true);
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53 fi
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54 &&
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55 \$WINE msconvert ${inputmask}
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56
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57 --outdir outputs
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58 --${output_type}
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59 $general_options.combineIonMobilitySpectra
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60 $general_options.simAsSpectra
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61 $general_options.srmAsSpectra
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62 $general_options.acceptZeroLengthSpectra
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63 $general_options.ignoreUnknownInstrumentError
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64
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65 #if $general_options.scan_summing.do_scan_summing == "true":
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66 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol"
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67 #end if
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68
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69 #if $general_options.multi_run_output.do_multi_run_output == "true":
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70 #if len($general_options.multi_run_output.run_index_set) > 0
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71 --runIndexSet "
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72 #for $index in $general_options.multi_run_output.run_index_set
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73 [${index.from},${index.to}]
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74 #end for
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75 "
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76 #end if
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77 #else
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78 --runIndexSet $general_options.multi_run_output.runIndexSet
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79 #end if
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80
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81 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests
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82 --stripLocationFromSourceFiles
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83
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84 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
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85 #if $data_processing.peak_picking.pick_peaks == "true"
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86 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
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87 #end if
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88
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89 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
9
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90 --filter "mzRefiner $input_ident_name
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91 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
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92 thresholdScore=$data_processing.precursor_refinement.thresholdScore
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93 thresholdValue=$data_processing.precursor_refinement.thresholdValue
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94 thresholdStep=$data_processing.precursor_refinement.thresholdStep
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95 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1"
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96 #end if
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97
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98 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
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99 --filter "chargeStatePredictor
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100 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
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101 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
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102 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
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103 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
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104 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
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105 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
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106 --filter "turbocharger
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107 minCharge=$data_processing.charge_state_calculation.minCharge
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108 maxCharge=$data_processing.charge_state_calculation.maxCharge
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109 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
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110 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
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111 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
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112 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
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113 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
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114 #end if
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115
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116 #for threshold_entry in $data_processing.thresholds
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117 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
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118 #end for
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119
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120 #if $data_processing.filter_mz_windows.do_mzwindow_filter == "true"
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121 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
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122 #end if
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123
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124 #if $data_processing.etd_filtering.do_etd_filtering == "true"
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125 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
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126 $data_processing.etd_filtering.remove_charge_reduced
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127 $data_processing.etd_filtering.remove_neutral_loss
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128 $data_processing.etd_filtering.blanket_removal
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129 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units"
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130 #end if
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131
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132 #if $data_processing.ms2denoise.denoise == "true"
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133 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
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134 #end if
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135
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136 #if str($data_processing.ms2deisotope) == "true"
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137 --filter "MS2Deisotope"
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138 #end if
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139
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140 #if $data_processing.demultiplex.demultiplex_on == "true"
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9b61227976d6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"
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141 --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize"
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142 #end if
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143
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144 ## SCAN INCLUSION/EXCLUSION FILTERS
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145 #if str($filtering.activation) != "false"
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146 --filter "activation $filtering.activation"
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147 #end if
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148
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149 #if len($filtering.indices) > 0
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150 --filter "index
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151 #for $index in $filtering.indices
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152 [${index.from},${index.to}]
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153 #end for
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154 "
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155 #end if
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156
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157 #if len($filtering.scan_numbers) > 0
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158 --filter "scanNumber
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159 #for $scan_number in $filtering.scan_numbers
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160 [${scan_number.from},${scan_number.to}]
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161 #end for
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162 "
9
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163 #end if
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164
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165 #if $filtering.strip_it.value
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166 --filter "stripIT"
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167 #end if
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168
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169 #if $filtering.filter_ms_levels.do_ms_level_filter == "true"
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170 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
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171 #end if
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172
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173 #if str($filtering.polarity) != "false"
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174 --filter "polarity $filtering.polarity"
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175 #end if
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176
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177 #if str($filtering.analyzer) != "false"
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178 --filter "analyzer $filtering.analyzer"
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179 #end if
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3cf310697624 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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180
3cf310697624 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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181 ## OUTPUT ENCODING
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182 #set $mz_encoding = str($settings.mz_encoding)
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183 #set $intensity_encoding = str($settings.intensity_encoding)
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184 #if $mz_encoding == $intensity_encoding
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185 #if $mz_encoding == "64"
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186 --64
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187 #else
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188 --32
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189 #end if
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190 #else
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191 --mz${mz_encoding}
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192 --inten${intensity_encoding}
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193 #end if
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194
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195 #set binary_compression = str($settings.binary_compression)
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196 #if $binary_compression == "zlib"
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197 --zlib
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198 #else if $binary_compression == "numpressLinearPic"
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199 --numpressLinear --numpressPic
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200 #else if $binary_compression == "numpressLinearSlof"
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201 --numpressLinear --numpressSlof
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202 #else if $binary_compression == "numpressLinear"
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203 --numpressLinear
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204 #else if $binary_compression == "numpressPic"
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205 --numpressPic
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206 #else if $binary_compression == "numpressSlof"
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207 --numpressSlof
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208 #end if
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209
18
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210 #if $settings.gzip_compression == "true"
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211 --gzip
9
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212 #end if
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213
10
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214 #if $general_options.multi_run_output.do_multi_run_output == 'false':
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215 --outfile '${os.path.splitext($basename)[0]}'
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216 #end if
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217 &&
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218 if [ "\$CAN_SUDO" -eq "0" ]; then
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219 sudo chown -R \$uid:\$gid './';
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220 fi
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221 #if $general_options.multi_run_output.do_multi_run_output == 'false':
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222 && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'
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223 #else
15
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224 ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file
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225 ## this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803
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226 #if $output_type == 'mzML' or $output_type == 'mzXML'
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227 && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower()
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228 ## a newline is needed after `#echo ...` therefore the `;'` on the next line
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229 ;'
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230 #end if
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231 #end if
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232
17
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233 #if $data_processing.precursor_refinement.use_mzrefinement == "true"
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234 && mv '$output_refinement_name' '$output_refinement';
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235 #end if
9
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236 ]]>
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237 </command>
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238 </xml>
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239
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240 <xml name="msconvertInputParameters">
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241 <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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242 <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator>
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243 </param>
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244
9
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245 <param name="output_type" type="select" label="Output Type">
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246 <option value="mz5" selected="true">mz5</option>
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247 <option value="mzML">mzML</option>
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248 <option value="mzXML">mzXML</option>
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249 <option value="mgf">mgf</option>
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250 <option value="ms2">ms2</option>
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251 </param>
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252
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253 <section name="data_processing" title="Data Processing Filters">
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254 <conditional name="peak_picking">
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255 <param type="select" name="pick_peaks" label="Apply peak picking?">
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256 <option value="true">Yes</option>
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257 <option value="false" selected="true">No</option>
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258 </param>
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259 <when value="false" />
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260 <when value="true">
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261 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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262 <option value="1">MS1 Only (1)</option>
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263 <option value="2">MS2 Only (2)</option>
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264 <option value="2-">MS2 and on (2-)</option>
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265 <option value="1-" selected="true">All Levels (1-)</option>
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266 </param>
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267 <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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268 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
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269 <option value="cwt">CantWaiT - continuous wavelet transform</option>
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270 </param>
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271 </when>
9
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272 </conditional>
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273
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274 <conditional name="precursor_refinement">
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275 <param type="select" name="use_mzrefinement" label="Apply m/z refinement with identification data?">
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276 <option value="true">Yes</option>
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277 <option value="false" selected="true">No</option>
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278 </param>
9
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279 <when value="false"></when>
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280 <when value="true">
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281 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
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282 <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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283 <sanitizer>
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284 <valid initial="string.letters" />
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285 </sanitizer>
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286 </param>
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287 <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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288 <sanitizer>
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289 <valid initial="string.letters,string.digits">
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290 <add value="-" />
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291 </valid>
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292 </sanitizer>
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293 </param>
9
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294 <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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295 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
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296 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
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297 <option value="1">MS1 Only (1)</option>
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298 <option value="2">MS2 Only (2)</option>
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299 <option value="2-">MS2 and on (2-)</option>
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300 <option value="1-" selected="true">All Levels (1-)</option>
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301 </param>
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302 </when>
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303 </conditional>
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304
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305 <conditional name="charge_state_calculation">
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306 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
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307 <option value="false">no</option>
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308 <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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309 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
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310 </param>
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311 <when value="false" />
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312 <when value="predictor">
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313 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
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314 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
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315 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
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316 <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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317 <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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318 </when>
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319 <when value="turbocharger">
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320 <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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321 <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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322 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
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323 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
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324 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
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325 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
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326 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
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327 </when>
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328 </conditional>
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329
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330 <repeat name="thresholds" title="Filter by Threshold">
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331 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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332 <option value="count">Peak count</option>
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333 <option value="count-after-ties">Peak count (after ties)</option>
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334 <option value="absolute">Peak absolute intensity</option>
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335 <option value="bpi-relative">Fraction of base peak intensity</option>
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336 <option value="tic-relative">Fraction of total ion current</option>
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337 <option value="tic-fraction">Aggregate fraction of total ion current</option>
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338 </param>
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339 <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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340 <param type="select" label="Keep" name="orientation">
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341 <option value="most-intense">Most intense peaks</option>
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342 <option value="least-intense">Least intense peaks</option>
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343 </param>
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344 </repeat>
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345
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346 <conditional name="filter_mz_windows">
16
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347 <param name="do_mzwindow_filter" type="select" label="Filter m/z Window" help="">
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348 <option value="true">Yes</option>
18
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349 <option value="false" selected="true">No</option>
16
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350 </param>
9
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351 <when value="false" />
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352 <when value="true">
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353 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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354 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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355 </when>
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356 </conditional>
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357
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358 <conditional name="etd_filtering">
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359 <param type="select" name="do_etd_filtering" label="Filter out ETD precursor peaks?">
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360 <option value="true">Yes</option>
18
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361 <option value="false" selected="true">No</option>
16
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362 </param>
9
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363 <when value="false" />
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364 <when value="true">
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365 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
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366 <option value="true" selected="true">yes</option>
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367 <option value="false">no</option>
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368 </param>
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369 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
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370 <option value="true" selected="true">yes</option>
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371 <option value="false">no</option>
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372 </param>
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373 <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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374 <option value="true" selected="true">yes</option>
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375 <option value="false">no</option>
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376 </param>
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377 <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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378 <option value="true" selected="true">yes</option>
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379 <option value="false">no</option>
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380 </param>
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381 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
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382 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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383 <option value="MZ" selected="true">mz</option>
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384 <option value="PPM">ppm</option>
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385 </param>
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386 </when>
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387 </conditional>
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388
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389 <conditional name="ms2denoise">
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390 <param name="denoise" type="select" label="De-noise MS2 with moving window filter">
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391 <option value="true">Yes</option>
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392 <option value="false" selected="true">No</option>
16
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393 </param>
9
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394 <when value="true">
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395 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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396 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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397 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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398 </when>
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parents:
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399 <when value="false" />
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parents:
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400 </conditional>
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401
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402 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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403
13
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404 <conditional name="demultiplex">
16
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405 <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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406 <option value="true">Yes</option>
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407 <option value="false" selected="true">No</option>
16
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408 </param>
13
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409 <when value="true">
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410 <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
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411 <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
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412 <option value="MZ">mz</option>
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413 <option value="PPM" selected="true">ppm</option>
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414 </param>
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415 <param name="nnlsMaxIter" type="integer" label="Maximum iterations for NNLS solve" value="50"/>
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416 <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
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417 <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"/>
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418 <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
16
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419 <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"/>
13
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420 <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
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421 <option value="none" selected="true">None</option>
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422 <option value="overlap_only">Overlap only</option>
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423 </param>
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424 <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
16
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425 <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"/>
13
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426 <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
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427 </when>
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428 <when value="false" />
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429 </conditional>
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430
9
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431 </section>
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432
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433
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434 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
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435
9
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436 <param name="activation" type="select" label="Filter by Activation">
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437 <option value="false" selected="true">no</option>
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438 <option value="ETD">ETD</option>
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439 <option value="CID">CID</option>
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440 <option value="SA">SA</option>
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441 <option value="HCD">HCD</option>
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442 <option value="BIRD">BIRD</option>
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443 <option value="ECD">ECD</option>
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444 <option value="IRMPD">IRMPD</option>
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445 <option value="PD">PD</option>
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446 <option value="PSD">PSD</option>
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447 <option value="PQD">PQD</option>
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448 <option value="SID">SID</option>
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449 <option value="SORI">SORI</option>
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450 </param>
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451
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452 <repeat name="indices" title="Filter Scan Indices">
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453 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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454 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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455 </repeat>
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456
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457 <repeat name="scan_numbers" title="Filter Scan Numbers">
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458 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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459 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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460 </repeat>
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461
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462 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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463
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464 <conditional name="filter_ms_levels">
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465 <param name="do_ms_level_filter" type="select" label="Filter MS Levels">
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466 <option value="true">Yes</option>
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467 <option value="false" selected="true">No</option>
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468 </param>
9
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469 <when value="false" />
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470 <when value="true">
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471 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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472 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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473 </when>
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474 </conditional>
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475
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476 <param name="polarity" type="select" label="Filter by Polarity">
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477 <option value="false" selected="true">no</option>
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478 <option value="positive">positive</option>
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479 <option value="negative">negative</option>
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480 </param>
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481
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482 <param name="analyzer" type="select" label="Filter by Analyzer">
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483 <option value="false" selected="true">no</option>
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484 <option value="quad">Quadrupole</option>
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485 <option value="orbi">Orbitrap</option>
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486 <option value="FT">Fourier-transform</option>
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487 <option value="IT">Ion trap</option>
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diff changeset
488 <option value="TOF">Time of flight</option>
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489 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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490 </section>
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491
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492 <section name="general_options" title="General Options">
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493 <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." />
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494
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495 <conditional name="scan_summing">
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496 <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">
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
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497 <option value="true">Yes</option>
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498 <option value="false" selected="true">No</option>
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499 </param>
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500 <when value="false" />
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501 <when value="true">
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502 <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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503 <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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504 <param name="ionMobilityTol" type="float" label="Ion mobility tolerance" value="0.01" min="0" optional="true" help="Spectra with ion mobility values with a difference less than this tolerance are summed together. Only relevant for ion mobility spectra." />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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505 </when>
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506 </conditional>
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507
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diff changeset
508 <param argument="--simAsSpectra" type="boolean" truevalue="--simAsSpectra" falsevalue="" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" />
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509 <param argument="--srmAsSpectra" type="boolean" truevalue="--srmAsSpectra" falsevalue="" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" />
3cf310697624 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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510 <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" />
3cf310697624 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 79157337a253a1c2fce2ad1739668c66b6c54df1"
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511 <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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parents: 9
diff changeset
512
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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513 <conditional name="multi_run_output">
16
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diff changeset
514 <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)">
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diff changeset
515 <option value="true">Yes</option>
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diff changeset
516 <option value="false" selected="true">No</option>
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517 </param>
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518 <when value="false">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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519 <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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520 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
521 <when value="true">
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diff changeset
522 <repeat name="run_index_set" title="Select runs for multi-run sources" help="For multi-run sources (e.g. WIFF), select only the specified run indices">
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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523 <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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parents: 9
diff changeset
524 <param name="to" type="integer" label="Run Index To" value="0" min="0" optional="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
525 </repeat>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
526 </when>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
527 </conditional>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
528 </section>
9
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529
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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530 <section name="settings" title="Output Encoding Settings">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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531 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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532 <option value="64" selected="true">64</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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533 <option value="32">32</option>
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534 </param>
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535 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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536 <option value="64">64</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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537 <option value="32" selected="true">32</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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538 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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539 <param type="select" name="binary_compression" label="Binary data compression">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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540 <option value="false">None</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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541 <option value="zlib" selected="true">zlib</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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542 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
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543 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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544 <option value="numpressLinear">numpressLinear only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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diff changeset
545 <option value="numpressPic">numpressPic only</option>
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546 <option value="numpressSlof">numpressSlof only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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547 </param>
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548 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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549 </section>
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550 </xml>
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551
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552 <xml name="msconvertOutput">
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553 <outputs>
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554 <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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555 <filter>general_options['multi_run_output']['do_multi_run_output'] == "false"</filter>
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diff changeset
556 <change_format>
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557 <when input="output_type" value="mz5" format="mz5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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558 <when input="output_type" value="mzXML" format="mzxml" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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559 <when input="output_type" value="ms2" format="ms2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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diff changeset
560 <when input="output_type" value="mgf" format="mgf" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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561 </change_format>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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562 </data>
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563 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv">
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diff changeset
564 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == "true"</filter>
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dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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565 </data>
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diff changeset
566 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type} collection">
17
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parents: 16
diff changeset
567 <filter>general_options['multi_run_output']['do_multi_run_output'] == "true"</filter>
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
568 <discover_datasets pattern="__name_and_ext__" directory="outputs" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
569 </collection>
9
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diff changeset
570 </outputs>
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parents:
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571 </xml>
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parents:
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572
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parents:
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573
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parents:
diff changeset
574 <xml name="msconvert_tests">
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diff changeset
575 <test expect_num_outputs="1">
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diff changeset
576 <param name="input" value="small.RAW" ftype="thermo.raw" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
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diff changeset
577 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
578 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
579 <param name="data_processing|peak_picking|pick_peaks" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
580 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
581 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
582 <output name="output" file="small-peakpicking-vendor-allMS.mzML" ftype="mzml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
583 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
584 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
585 <param name="input" value="ThyroglobMRM000003.d.tar" ftype="brukertdf.d.tar" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
586 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
587 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
588 <param name="general_options|combineIonMobilitySpectra" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
589 <param name="general_options|scan_summing|do_scan_summing" value="true" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
590 <output name="output" file="ThyroglobMRM000003.mzML" ftype="mzml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
591 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
592 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
593 <param name="input" value="MassLynxTest.raw.tar" ftype="watersmasslynx.raw.tar" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
594 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
595 <param name="output_type" value="mzML" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
596 <output name="output" file="MassLynxTest.mzML" ftype="mzml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
597 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
598 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
599 <param name="input" value="AgilentMassHunterTest.d.tar" ftype="agilentmasshunter.d.tar" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
600 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
601 <param name="output_type" value="mzXML" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
602 <output name="output" file="AgilentMassHunterTest.mzXML" ftype="mzxml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
603 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
604 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
605 <param name="input" value="BrukerBafTest.d.tar" ftype="brukerbaf.d.tar" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
606 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
607 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
608 <param name="data_processing|peak_picking|pick_peaks" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
609 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="vendor" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
610 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1-" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
611 <output name="output" file="BrukerBafTest.mzML" ftype="mzml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
612 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
613 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
614 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
615 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
616 <param name="output_type" value="mzXML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
617 <param name="general_options|multi_run_output|do_multi_run_output" value="false" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
618 <param name="general_options|multi_run_output|runIndexSet" value="1" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
619 <param name="filtering|indices_0|from" value="0" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
620 <param name="filtering|indices_0|to" value="499" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
621 <param name="general_options|srmAsSpectra" value="true" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
622 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" ftype="mzxml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
623 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
624 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
625 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
626 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
627 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
628 <param name="general_options|multi_run_output|do_multi_run_output" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
629 <param name="general_options|multi_run_output|run_index_set_0|from" value="0" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
630 <param name="general_options|multi_run_output|run_index_set_0|to" value="1" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
631 <output_collection name="multi_run_output_list" type="list">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
632 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
633 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
634 </output_collection>
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
635 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
636 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
637 <param name="input" value="SciexTest.wiff.tar" ftype="wiff.tar" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
638 <param name="license_agreement" value="true" />
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
639 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
640 <param name="general_options|multi_run_output|do_multi_run_output" value="true" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
641 <output_collection name="multi_run_output_list" type="list">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
642 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" ftype="mzml" lines_diff="4" />
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
643 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" ftype="mzml" lines_diff="4" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
644 </output_collection>
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
645 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
646
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
647 <!-- this data file only has profile MS1, so the result is the same -->
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
648 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
649 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
650 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
651 <param name="output_type" value="mz5" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
652 <param name="settings|mz_encoding" value="64" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
653 <param name="settings|intensity_encoding" value="64" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
654 <output name="output" file="small-zlib-64.mz5" compare="sim_size" ftype="mz5" delta="150000" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
655 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
656 <!-- TODO: how to test gzipped output?
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
657 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
658 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
659 <param name="output_type" value="mzXML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
660 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
661 <param name="intensity_encoding" value="32" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
662 <param name="settings|binary_compression" value="false" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
663 <param name="gzip_compression" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
664 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
665 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
666 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
667 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
668 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
669 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
670 <param name="intensity_encoding" value="32" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
671 <param name="settings|binary_compression" value="false" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
672 <param name="gzip_compression" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
673 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
674 </test>-->
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
675 <test expect_num_outputs="2">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
676 <param name="input" value="Rpal_01.mz5" ftype="mz5" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
677 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
678 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
679 <param name="settings|binary_compression" value="numpressLinearPic" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
680 <param name="data_processing|precursor_refinement|use_mzrefinement" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
681 <param name="data_processing|precursor_refinement|input_ident" value="Rpal_01.pepXML" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
682 <param name="data_processing|precursor_refinement|thresholdScore" value="mvh" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
683 <param name="data_processing|precursor_refinement|thresholdValue" value="40-" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
684 <output name="output" file="Rpal_01-mzRefinement.mzML" ftype="mzml" compare="sim_size" delta="0" />
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
685 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" ftype="tsv" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
686 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
687 <test expect_num_outputs="1">
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
688 <param name="input" value="small.mzML" ftype="mzml" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
689 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
690 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
691
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
692 <param name="data_processing|peak_picking|pick_peaks" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
693 <param name="data_processing|peak_picking|pick_peaks_algorithm" value="cwt" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
694 <param name="data_processing|peak_picking|pick_peaks_ms_levels" value="1" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
695
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
696 <param name="data_processing|thresholds_0|threshold_type" value="count" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
697 <param name="data_processing|thresholds_0|value" value="100" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
698 <param name="data_processing|thresholds_0|orientation" value="most-intense" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
699 <param name="data_processing|thresholds_1|threshold_type" value="absolute" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
700 <param name="data_processing|thresholds_1|value" value="1" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
701 <param name="data_processing|thresholds_1|orientation" value="most-intense" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
702
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
703 <param name="data_processing|filter_mz_windows|do_mzwindow_filter" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
704 <param name="data_processing|filter_mz_windows|mz_window_from" value="420" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
705 <param name="data_processing|filter_mz_windows|mz_window_to" value="840" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
706
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
707 <param name="filtering|indices_0|from" value="0" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
708 <param name="filtering|indices_0|to" value="20" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
709 <param name="filtering|indices_1|from" value="41" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
710 <param name="filtering|indices_1|to" value="41" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
711
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
712 <param name="filtering|filter_ms_levels|do_ms_level_filter" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
713 <param name="filtering|filter_ms_levels|ms_level_from" value="2" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
714 <param name="filtering|filter_ms_levels|ms_level_to" value="2" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
715
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
716 <param name="filtering|scan_numbers_0|from" value="5" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
717 <param name="filtering|scan_numbers_0|to" value="25" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
718 <param name="filtering|scan_numbers_1|from" value="40" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
719 <param name="filtering|scan_numbers_1|to" value="40" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
720
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
721 <param name="data_processing|ms2deisotope" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
722
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
723 <param name="data_processing|ms2denoise|denoise" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
724 <param name="data_processing|ms2denoise|num_peaks" value="10" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
725 <param name="data_processing|ms2denoise|window_width" value="40" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
726 <param name="data_processing|ms2denoise|relax" value="false" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
727
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
728 <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="predictor" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
729 <param name="data_processing|charge_state_calculation|predictor_overrideExistingCharge" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
730 <param name="data_processing|charge_state_calculation|minMultipleCharge" value="2" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
731 <param name="data_processing|charge_state_calculation|maxMultipleCharge" value="5" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
732 <param name="data_processing|charge_state_calculation|singleChargeFractionTIC" value="0.95" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
733 <param name="data_processing|charge_state_calculation|maxKnownCharge" value="8" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
734
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
735 <param name="settings|mz_encoding" value="32" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
736 <param name="settings|intensity_encoding" value="32" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
737
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
738 <param name="settings|binary_compression" value="numpressLinearPic" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
739 <output name="output" file="small-composite-test.mzML" ftype="mzml" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
740 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
741 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
742 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
743 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
744 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
745 <param name="settings|binary_compression" value="numpressLinearPic" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
746 <param name="data_processing|charge_state_calculation|charge_state_calculation_method" value="turbocharger" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
747 <param name="data_processing|charge_state_calculation|minCharge" value="1" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
748 <param name="data_processing|charge_state_calculation|maxCharge" value="5" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
749 <param name="data_processing|charge_state_calculation|precursorsBefore" value="1" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
750 <param name="data_processing|charge_state_calculation|precursorsAfter" value="1" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
751 <param name="data_processing|charge_state_calculation|halfIsoWidth" value="1.5" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
752 <param name="data_processing|charge_state_calculation|defaultMinCharge" value="1" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
753 <param name="data_processing|charge_state_calculation|defaultMaxCharge" value="5" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
754 <param name="filtering|strip_it" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
755 <output name="output" file="small-composite-test-2.mzML" ftype="mzml" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
756 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
757 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
758 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
759 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
760 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
761 <param name="filtering|activation" value="CID" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
762 <param name="settings|binary_compression" value="numpressLinearPic" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
763 <output name="output" file="small-activation.mzML" lines_diff="114" ftype="mzml" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
764 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
765 <test expect_num_outputs="1">
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
766 <param name="input" value="small-peakpicking-cwt-allMS.mzML" ftype="mzml" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
767 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
768 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
769 <param name="filtering|polarity" value="positive" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
770 <param name="settings|binary_compression" value="numpressLinearPic" />
15
6153e8ada1ee "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877"
galaxyp
parents: 14
diff changeset
771 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" ftype="mzml" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
772 </test>
16
545054b15d7c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
galaxyp
parents: 15
diff changeset
773 <test expect_num_outputs="1">
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
774 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" ftype="mz5" />
10
9d5de24e6ef7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
galaxyp
parents: 9
diff changeset
775 <param name="license_agreement" value="true" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
776 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
777 <param name="data_processing|etd_filtering|do_etd_filtering" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
778 <param name="data_processing|etd_filtering|remove_precursor" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
779 <param name="data_processing|etd_filtering|remove_charge_reduced" value="true" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
780 <param name="data_processing|etd_filtering|remove_neutral_loss" value="false" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
781 <param name="data_processing|etd_filtering|blanket_removal" value="false" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
782 <param name="data_processing|etd_filtering|matching_tolerance" value="50" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
783 <param name="data_processing|etd_filtering|matching_tolerance_units" value="PPM" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
784 <param name="settings|binary_compression" value="numpressLinearPic" />
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
785 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" ftype="mzml" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
786 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
787 <!--<test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
788 <param name="input" value="small.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
789 <param name="output_type" value="mzML" />
18
331a50e8fd2f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
parents: 17
diff changeset
790 <param name="settings|binary_compression" value="numpressLinearPic" />
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
791 <output name="output" file="small-deisotope-poisson.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
792 </test>-->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
793 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
794 <xml name="citations">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
795 <citations>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
796 <citation type="doi">10.1093/bioinformatics/btn323</citation>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
797 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
798 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
799 </citations>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
800 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
801
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
802 </macros>