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annotate msconvert_macros.xml @ 2:c9b96a178758 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 532424dd138aa77ec59704fb5680f5ed0e2195f3
author galaxyp
date Tue, 14 Mar 2017 17:48:15 -0400
parents 7016f1f10f42
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <macros>
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2 <xml name="generic_requirements">
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3 <requirements>
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4 <requirement type="package" version="3.0.9992">proteowizard</requirement>
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5 </requirements>
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6 </xml>
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7 <token name="@VERSION@">3.0.9992</token>
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9 <xml name="msconvertCommand">
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10 <command interpreter="python">
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11 <![CDATA[
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12 #import re
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13 #set $ext = $input.ext
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15 ## sanitize display name for use as temp filename
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16 #set basename = 'pwiz_in'
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18 #if hasattr($input, 'display_name')
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19 ## explicit inclusion or exclusion ??
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20 #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.display_name)
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21 ##set basename = $re.sub(r'[\/\\\;\|\&\>\<]','_',$input.display_name)
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22 #end if
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23
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24 msconvert_wrapper.py
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26 #if $ext == 'wiff':
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27 --input='${input.extra_files_path}/wiff'
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28 --input_name='${basename}.wiff'
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29 --implicit='${input.extra_files_path}/wiff_scan'
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30 --input='${input.extra_files_path}/wiff_scan'
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31 --input_name='${basename}.wiff.scan'
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32 #else
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33 --input='${input}'
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34 --input_name='$basename'
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35 #end if
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36 --output='${output}'
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37 ## BEGIN_VERSION_DEFAULT
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38 --fromextension=$ext
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39 ## END_VERSION_DEFAULT
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40 --toextension=${output_type}
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42 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
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43 #if $data_processing.precursor_refinement.use_mzrefinement
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44 #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))
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45 --ident='$data_processing.precursor_refinement.input_ident'
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46 --ident_name='$input_ident_name'
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47 --refinement='$output_refinement'
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48 --filter "mzRefiner $input_ident_name
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49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
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50 thresholdScore=$data_processing.precursor_refinement.thresholdScore
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51 thresholdValue=$data_processing.precursor_refinement.thresholdValue
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52 thresholdStep=$data_processing.precursor_refinement.thresholdStep
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53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
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54 #end if
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55
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56 #if $data_processing.peak_picking.pick_peaks
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57 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
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58 #end if
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59
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60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
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61 --filter "chargeStatePredictor
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62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
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63 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
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64 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
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65 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
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66 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
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67 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
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68 --filter "turbocharger
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69 minCharge=$data_processing.charge_state_calculation.minCharge
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70 maxCharge=$data_processing.charge_state_calculation.maxCharge
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71 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
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72 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
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73 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
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74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
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75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
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76 #end if
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77
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78 #for threshold_entry in $data_processing.thresholds
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79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
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80 #end for
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81
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82 #if $data_processing.filter_mz_windows.do_mzwindow_filter
1
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83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
0
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84 #end if
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85
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86 #if $data_processing.etd_filtering.do_etd_filtering
1
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87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
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88 $data_processing.etd_filtering.remove_charge_reduced
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89 $data_processing.etd_filtering.remove_neutral_loss
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90 $data_processing.etd_filtering.blanket_removal
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91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
0
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92 #end if
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93
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94 #if $data_processing.ms2denoise.denoise
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95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
0
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96 #end if
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97
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98 #if str($data_processing.ms2deisotope) == "true"
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99 --filter "MS2Deisotope"
0
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100 #end if
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101
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102
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103 ## SCAN INCLUSION/EXCLUSION FILTERS
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104 #if str($filtering.activation) != "false"
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105 --filter "activation $filtering.activation"
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106 #end if
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107
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108 #if len($filtering.indices) > 0
1
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109 --filter "index
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110 #for $index in $filtering.indices
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111 [${index.from},${index.to}]
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112 #end for
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113 "
0
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114 #end if
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115
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116 #if len($filtering.scan_numbers) > 0
1
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117 --filter "scanNumber
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118 #for $scan_number in $filtering.scan_numbers
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119 [${scan_number.from},${scan_number.to}]
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120 #end for
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121 "
0
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122 #end if
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123
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124 #if $filtering.strip_it.value
1
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125 --filter "stripIT"
0
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126 #end if
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127
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128 #if $filtering.filter_ms_levels.do_ms_level_filter
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129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
0
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130 #end if
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131
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132 #if str($filtering.polarity) != "false"
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133 --filter "polarity $filtering.polarity"
0
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134 #end if
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135
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136 #if str($filtering.analyzer) != "false"
1
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137 --filter "analyzer $filtering.analyzer"
0
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138 #end if
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139
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140 ## OUTPUT ENCODING
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141 --
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142 #set $mz_encoding = str($settings.mz_encoding)
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143 #set $intensity_encoding = str($settings.intensity_encoding)
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144 #if $mz_encoding == $intensity_encoding
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145 #if $mz_encoding == "64"
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146 --64
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147 #else
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148 --32
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149 #end if
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150 #else
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151 --mz${mz_encoding}
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152 --inten${intensity_encoding}
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153 #end if
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154
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155 #set binary_compression = str($settings.binary_compression)
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156 #if $binary_compression == "zlib"
1
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157 --zlib
0
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158 #else if $binary_compression == "numpressLinearPic"
1
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159 --numpressLinear --numpressPic
0
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160 #else if $binary_compression == "numpressLinearSlof"
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161 --numpressLinear --numpressSlof
0
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162 #else if $binary_compression == "numpressLinear"
1
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163 --numpressLinear
0
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164 #else if $binary_compression == "numpressPic"
1
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165 --numpressPic
0
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166 #else if $binary_compression == "numpressSlof"
1
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167 --numpressSlof
0
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168 #end if
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169
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170 #if $settings.gzip_compression
1
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171 --gzip
0
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172 #end if
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173
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174 ]]>
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175 </command>
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176 </xml>
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177
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178 <xml name="msconvertInputParameters">
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179 <param name="output_type" type="select" label="Output Type">
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180 <option value="mz5" selected="true">mz5</option>
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181 <option value="mzML">mzML</option>
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182 <option value="mzXML">mzXML</option>
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183 <option value="mgf">mgf</option>
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184 <option value="ms2">ms2</option>
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185 </param>
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186
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187 <section name="data_processing" title="Data Processing Filters">
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188
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189 <conditional name="peak_picking">
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190 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
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191 <when value="false" />
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192 <when value="true">
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193 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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194 <option value="1">MS1 Only (1)</option>
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195 <option value="2">MS2 Only (2)</option>
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196 <option value="2-">MS2 and on (2-)</option>
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197 <option value="1-" selected="true">All Levels (1-)</option>
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198 </param>
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199 <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
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200 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
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201 <option value="cwt">CantWaiT - continuous wavelet transform</option>
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202 </param>
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203 </when>
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204 </conditional>
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205
1
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206 <conditional name="precursor_refinement">
0
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207 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
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208 <when value="false"></when>
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209 <when value="true">
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210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
1
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211 <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+">
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212 <sanitizer>
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213 <valid initial="string.letters" />
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214 </sanitizer>
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215 </param>
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216 <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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217 <sanitizer>
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218 <valid initial="string.letters,string.digits">
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219 <add value="-" />
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220 </valid>
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221 </sanitizer>
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222 </param>
0
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223 <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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224 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
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225 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
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226 <option value="1">MS1 Only (1)</option>
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227 <option value="2">MS2 Only (2)</option>
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228 <option value="2-">MS2 and on (2-)</option>
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229 <option value="1-" selected="true">All Levels (1-)</option>
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230 </param>
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231 </when>
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232 </conditional>
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233
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234 <conditional name="charge_state_calculation">
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235 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
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236 <option value="false">no</option>
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237 <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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238 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
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239 </param>
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240 <when value="false" />
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241 <when value="predictor">
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242 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
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243 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
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244 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
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245 <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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246 <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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247 </when>
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248 <when value="turbocharger">
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249 <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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250 <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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251 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
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252 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
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253 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
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254 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
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255 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
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256 </when>
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257 </conditional>
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258
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259 <repeat name="thresholds" title="Filter by Threshold">
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260 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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261 <option value="count">Peak count</option>
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262 <option value="count-after-ties">Peak count (after ties)</option>
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263 <option value="absolute">Peak absolute intensity</option>
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264 <option value="bpi-relative">Fraction of base peak intensity</option>
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265 <option value="tic-relative">Fraction of total ion current</option>
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266 <option value="tic-fraction">Aggregate fraction of total ion current</option>
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267 </param>
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268 <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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269 <param type="select" label="Keep" name="orientation">
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270 <option value="most-intense">Most intense peaks</option>
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271 <option value="least-intense">Least intense peaks</option>
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272 </param>
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273 </repeat>
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274
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275 <conditional name="filter_mz_windows">
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276 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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277 <when value="false" />
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278 <when value="true">
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279 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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280 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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281 </when>
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282 </conditional>
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283
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284 <conditional name="etd_filtering">
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285 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
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286 <when value="false" />
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287 <when value="true">
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288 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
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289 <option value="true" selected="true">yes</option>
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290 <option value="false">no</option>
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291 </param>
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292 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
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293 <option value="true" selected="true">yes</option>
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294 <option value="false">no</option>
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295 </param>
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296 <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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297 <option value="true" selected="true">yes</option>
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298 <option value="false">no</option>
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299 </param>
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300 <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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301 <option value="true" selected="true">yes</option>
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302 <option value="false">no</option>
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303 </param>
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304 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
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305 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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306 <option value="MZ" selected="true">mz</option>
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307 <option value="PPM">ppm</option>
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308 </param>
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309 </when>
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310 </conditional>
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311
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312 <conditional name="ms2denoise">
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313 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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314 <when value="true">
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315 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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316 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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317 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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318 </when>
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319 <when value="false" />
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320 </conditional>
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321
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322 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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323
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324 </section>
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325
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326
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327 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
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328
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329 <param name="activation" type="select" label="Filter by Activation">
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330 <option value="false" selected="true">no</option>
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galaxyp
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331 <option value="ETD">ETD</option>
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galaxyp
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332 <option value="CID">CID</option>
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galaxyp
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333 <option value="SA">SA</option>
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galaxyp
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334 <option value="HCD">HCD</option>
1
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galaxyp
parents: 0
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335 <option value="BIRD">BIRD</option>
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galaxyp
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336 <option value="ECD">ECD</option>
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
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337 <option value="IRMPD">IRMPD</option>
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galaxyp
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338 <option value="PD">PD</option>
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galaxyp
parents: 0
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339 <option value="PSD">PSD</option>
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galaxyp
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340 <option value="PQD">PQD</option>
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galaxyp
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341 <option value="SID">SID</option>
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galaxyp
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342 <option value="SORI">SORI</option>
0
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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343 </param>
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344
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
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345 <repeat name="indices" title="Filter Scan Indices">
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346 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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347 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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348 </repeat>
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349
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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350 <repeat name="scan_numbers" title="Filter Scan Numbers">
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351 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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352 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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353 </repeat>
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354
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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355 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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356
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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357 <conditional name="filter_ms_levels">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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358 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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359 <when value="false" />
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parents:
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360 <when value="true">
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361 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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362 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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363 </when>
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364 </conditional>
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parents:
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365
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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366 <param name="polarity" type="select" label="Filter by Polarity">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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367 <option value="false" selected="true">no</option>
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galaxyp
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368 <option value="positive">positive</option>
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galaxyp
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369 <option value="negative">negative</option>
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370 </param>
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galaxyp
parents:
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371
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
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372 <param name="analyzer" type="select" label="Filter by Analyzer">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
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373 <option value="false" selected="true">no</option>
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galaxyp
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374 <option value="quad">Quadrupole</option>
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galaxyp
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375 <option value="orbi">Orbitrap</option>
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galaxyp
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376 <option value="FT">Fourier-transform</option>
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galaxyp
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377 <option value="IT">Ion trap</option>
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galaxyp
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378 <option value="TOF">Time of flight</option>
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379 </param>
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380 </section>
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381
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
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382
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
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383 <section name="settings" title="Output Encoding Settings">
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galaxyp
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384 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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385 <option value="64" selected="true">64</option>
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galaxyp
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386 <option value="32">32</option>
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387 </param>
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388 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
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galaxyp
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389 <option value="64">64</option>
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galaxyp
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390 <option value="32" selected="true">32</option>
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391 </param>
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392 <param type="select" name="binary_compression" label="Binary data compression">
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393 <option value="false">None</option>
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394 <option value="zlib" selected="true">zlib</option>
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galaxyp
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395 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
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parents:
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396 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
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397 <option value="numpressLinear">numpressLinear only</option>
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398 <option value="numpressPic">numpressPic only</option>
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galaxyp
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399 <option value="numpressSlof">numpressSlof only</option>
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400 </param>
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401 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
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402 </section>
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403 </xml>
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parents:
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404
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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parents:
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405 <xml name="msconvertOutput">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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406 <outputs>
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407 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
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parents:
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408 <change_format>
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409 <when input="output_type" value="mz5" format="mz5" />
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410 <when input="output_type" value="mzXML" format="mzxml" />
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411 <when input="output_type" value="ms2" format="ms2" />
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412 <when input="output_type" value="mgf" format="mgf" />
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413 </change_format>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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414 </data>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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415 <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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416 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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417 </data>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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418 </outputs>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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419 </xml>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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420
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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421
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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422 <xml name="msconvert_tests">
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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423 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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424 <param name="input" value="small.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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425 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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426 <param name="pick_peaks" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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427 <param name="pick_peaks_algorithm" value="cwt" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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428 <param name="pick_peaks_ms_levels" value="1-" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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429 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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430 </test>
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431
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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432 <!-- this data file only has profile MS1, so the result is the same -->
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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433 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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434 <param name="input" value="small.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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435 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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436 <param name="pick_peaks" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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437 <param name="pick_peaks_algorithm" value="cwt" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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438 <param name="pick_peaks_ms_levels" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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439 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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440 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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441 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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442 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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443 <param name="output_type" value="mz5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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444 <param name="mz_encoding" value="64" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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445 <param name="intensity_encoding" value="64" />
1
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
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446 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
0
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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447 </test>
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448 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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449 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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450 <param name="output_type" value="mzXML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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451 <param name="mz_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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452 <param name="intensity_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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453 <output name="output" file="small-zlib-32.mzXML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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454 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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455 <!-- TODO: how to test gzipped output?
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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456 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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diff changeset
457 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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458 <param name="output_type" value="mzXML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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459 <param name="mz_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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460 <param name="intensity_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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461 <param name="binary_compression" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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462 <param name="gzip_compression" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
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463 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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diff changeset
464 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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465 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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466 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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467 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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468 <param name="mz_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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469 <param name="intensity_encoding" value="32" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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470 <param name="binary_compression" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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471 <param name="gzip_compression" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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472 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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473 </test>-->
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474
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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475 <test>
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476 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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477 <param name="output_type" value="mzML" />
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478 <param name="binary_compression" value="numpressLinearPic" />
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479 <output name="output" file="small-numpressLP.mzML" />
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480 </test>
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481
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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482 <test>
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483 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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484 <param name="output_type" value="mzML" />
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485 <param name="binary_compression" value="numpressLinearSlof" />
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486 <output name="output" file="small-numpressLS.mzML" />
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487 </test>
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488
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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489 <test>
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490 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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491 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
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492 <param name="binary_compression" value="numpressLinear" />
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493 <output name="output" file="small-numpressL.mzML" />
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diff changeset
494 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
495
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
496 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
497 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
498 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
499 <param name="binary_compression" value="numpressPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
500 <output name="output" file="small-numpressP.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
501 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
502
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
503 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
504 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
505 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
506 <param name="binary_compression" value="numpressSlof" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
507 <output name="output" file="small-numpressS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
508 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
509
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
510 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
511 <param name="input" value="Rpal_01.mz5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
512 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
513 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
514 <param name="use_mzrefinement" value="true" />
1
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 0
diff changeset
515 <param name="input_ident" value="Rpal_01.pepXML" />
0
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
516 <param name="thresholdScore" value="mvh" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
517 <param name="thresholdValue" value="40-" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
518 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
1
7016f1f10f42 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
galaxyp
parents: 0
diff changeset
519 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
0
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
520 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
521
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
522 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
523 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
524 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
525 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
526 <param name="charge_state_calculation_method" value="predictor" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
527 <param name="predictor_overrideExistingCharge" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
528 <param name="minMultipleCharge" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
529 <param name="maxMultipleCharge" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
530 <param name="singleChargeFractionTIC" value="0.95" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
531 <param name="maxKnownCharge" value="8" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
532 <output name="output" file="small-chargeStatePredictor.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
533 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
534 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
535 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
536 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
537 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
538 <param name="charge_state_calculation_method" value="turbocharger" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
539 <param name="minCharge" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
540 <param name="maxCharge" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
541 <param name="precursorsBefore" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
542 <param name="precursorsAfter" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
543 <param name="halfIsoWidth" value="1.5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
544 <param name="defaultMinCharge" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
545 <param name="defaultMaxCharge" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
546 <output name="output" file="small-turbocharger.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
547 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
548 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
549 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
550 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
551 <param name="do_etd_filtering" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
552 <param name="remove_precursor" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
553 <param name="remove_charge_reduced" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
554 <param name="remove_neutral_loss" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
555 <param name="blanket_removal" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
556 <param name="matching_tolerance" value="50" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
557 <param name="matching_tolerance_units" value="ppm" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
558 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
559 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
560 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
561 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
562 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
563 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
564 <param name="thresholds_0|threshold_type" value="count" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
565 <param name="thresholds_0|value" value="100" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
566 <param name="thresholds_0|orientation" value="most-intense" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
567 <param name="thresholds_1|threshold_type" value="absolute" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
568 <param name="thresholds_1|value" value="1" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
569 <param name="thresholds_1|orientation" value="most-intense" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
570 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
571 <output name="output" file="small-threshold.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
572 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
573 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
574 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
575 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
576 <param name="do_mzwindow_filter" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
577 <param name="mz_window_from" value="420" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
578 <param name="mz_window_to" value="840" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
579 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
580 <output name="output" file="small-mzWindow.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
581 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
582 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
583 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
584 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
585 <param name="denoise" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
586 <param name="num_peaks" value="10" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
587 <param name="window_width" value="40" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
588 <param name="relax" value="false" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
589 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
590 <output name="output" file="small-denoise.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
591 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
592 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
593 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
594 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
595 <param name="ms2deisotope" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
596 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
597 <output name="output" file="small-deisotope.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
598 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
599 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
600 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
601 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
602 <param name="activation" value="CID" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
603 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
604 <output name="output" file="small-activation.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
605 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
606 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
607 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
608 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
609 <param name="indices_0|from" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
610 <param name="indices_0|to" value="4" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
611 <param name="indices_1|from" value="10" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
612 <param name="indices_1|to" value="10" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
613 <param name="indices_2|from" value="13" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
614 <param name="indices_2|to" value="15" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
615 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
616 <output name="output" file="small-index-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
617 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
618 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
619 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
620 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
621 <param name="strip_it" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
622 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
623 <output name="output" file="small-strip-it.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
624 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
625 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
626 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
627 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
628 <param name="do_ms_level_filter" value="true" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
629 <param name="ms_level_from" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
630 <param name="ms_level_to" value="2" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
631 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
632 <output name="output" file="small-ms-level-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
633 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
634 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
635 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
636 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
637 <param name="polarity" value="positive" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
638 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
639 <output name="output" file="small-polarity-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
640 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
641 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
642 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
643 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
644 <param name="analyzer" value="IT" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
645 <param name="binary_compression" value="numpressLinearPic" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
646 <output name="output" file="small-analyzer-filter.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
647 </test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
648 <test>
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
649 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
650 <param name="output_type" value="mzML" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
651 <param name="scan_numbers_0|from" value="3" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
652 <param name="scan_numbers_0|to" value="5" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
653 <param name="scan_numbers_1|from" value="11" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
654 <param name="scan_numbers_1|to" value="11" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
diff changeset
655 <param name="scan_numbers_2|from" value="14" />
baa6c072fccc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 4fa5bf9c62e4bba06c4d6e7de962c85959b61579-dirty
galaxyp
parents:
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656 <param name="scan_numbers_2|to" value="16" />
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657 <param name="binary_compression" value="numpressLinearPic" />
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658 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
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659 </test>
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660 <!--<test>
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661 <param name="input" value="small.mzML" />
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662 <param name="output_type" value="mzML" />
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663 <param name="binary_compression" value="numpressLinearPic" />
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664 <output name="output" file="small-deisotope-poisson.mzML" />
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665 </test>-->
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666 </xml>
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667 <xml name="msconvert_help">
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668 **What it does**
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669
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670 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
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671
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672 You can view the original documentation here_.
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673
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674 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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675 </xml>
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676
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677 <xml name="citations">
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678 <citations>
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679 <citation type="doi">10.1093/bioinformatics/btn323</citation>
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680 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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681 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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682 </citations>
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683 </xml>
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684
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685 </macros>