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1 <tool id="msconvert$VERSION$DESCRIPTION" name="msconvert$VERSION$DESCRIPTION" version="0.1.0">
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2 <!-- BEGIN_VERSION_RAW -->
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3 <description>Convert and filter a Thermo Finnigan RAW file</description>
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4 <!-- END_VERSION_RAW -->
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5 <!-- BEGIN_VERSION_DEFAULT -->
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6 <description>Convert and filter a mass spec peak list</description>
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7 <!-- END_VERSION_DEFAULT -->
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8
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9 <command interpreter="python">
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10 msconvert_wrapper.py
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11 --input=${input}
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12 #if hasattr($input, 'display_name')
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13 --input_name='${input.display_name}'
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14 #end if
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15 --output=${output}
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16 ## BEGIN_VERSION_DEFAULT
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17 --fromextension=${input.ext}
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18 ## END_VERSION_DEFAULT
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19
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20 ## BEGIN_VERSION_RAW
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21 --fromextension=RAW
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22 ## END_VERSION_RAW
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23
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24 --toextension=${output_type}
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25
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26 #if $settings.settingsType == "full"
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27 --binaryencoding=${settings.binary_encoding}
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28 --mzencoding=${settings.mz_encoding}
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29 --intensityencoding=${settings.intensity_encoding}
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30 --zlib=${settings.zlib}
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31 #end if
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32
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33 #if $filtering.filtering_use
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34
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35 #if $filtering.precursor_recalculation.value
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36 --filter "precursorRecalculation"
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37 #end if
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38
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39 #if $filtering.peak_picking.pick_peaks
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40 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
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41 #end if
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42
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43 #if str($filtering.activation) != "false"
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44 --filter "activation $filtering.activation"
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45 #end if
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46
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47 #if len($filtering.indices) > 0
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48 --filter "index
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49 #for $index in $filtering.indices
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50 [${index.from},${index.to}]
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51 #end for
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52 "
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53 #end if
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54
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55 #if len($filtering.scan_numbers) > 0
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56 --filter "scanNumber
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57 #for $scan_number in $filtering.scan_numbers
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58 [${scan_number.from},${scan_number.to}]
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59 #end for
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60 "
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61 #end if
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62
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63 #for threshold_entry in $filtering.threshold_repeat
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64 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
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65 #end for
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66
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67
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68 #if $filtering.strip_it.value
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69 --filter "stripIT"
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70 #end if
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71
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72 #if $filtering.filter_mz_windows.do_filter
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73 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
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74 #end if
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75
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76
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77 #if $filtering.filter_ms_levels.do_filter
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78 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
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79 #end if
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80
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81 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
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82 --filter "ETDFilter"
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83 #end if
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84
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85 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
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86 --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units"
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87 #end if
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88
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89 ## BEGIN_VERSION_3
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90
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91 #if $filtering.precursor_refine.value
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92 --filter "precursorRefine"
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93 #end if
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94
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95 #if $filtering.ms2denoise.denoise
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96 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
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97 #end if
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98
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99 #if str($filtering.ms2deisotope) == "true"
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100 --filter "MS2Deisotope"
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101 #end if
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102
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103 #if str($filtering.polarity) != "false"
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104 --filter "polarity $filtering.polarity"
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105 #end if
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106
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107 #if str($filtering.analyzer) != "false"
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108 --filter "analyzer $filtering.analyzer"
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109 #end if
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110
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111 ## END_VERSION_3
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112
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113 #end if
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114
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115 </command>
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116
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117 <inputs>
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118 <!-- BEGIN_VERSION_RAW -->
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119 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
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120 <!-- END_VERSION_RAW -->
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121
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122 <!-- BEGIN_VERSION_DEFAULT -->
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123 <conditional name="type">
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124 <param name="input_type" type="select" label="Input Type">
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125 <option value="mzml">mzML</option>
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126 <option value="mzxml">mzXML</option>
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127 <option value="mgf">mgf</option>
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128 <option value="ms2">ms2</option>
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129 </param>
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130 <when value="mzml">
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131 <param format="mzml" name="input" type="data" label="Input mzML"/>
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132 </when>
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133 <when value="mzxml">
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134 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
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135 </when>
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136 <when value="mgf">
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137 <param format="mgf" name="input" type="data" label="Input mgf"/>
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138 </when>
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139 <when value="ms2">
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140 <param format="ms2" name="input" type="data" label="Input ms2"/>
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141 </when>
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142 </conditional>
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143 <!-- END_VERSION_DEFAULT -->
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144 <param name="output_type" type="select" label="Output Type">
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145 <option value="mzML">mzML (indexed)</option>
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146 <option value="unindexed_mzML">mzML (unindexed)</option>
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147 <option value="mzXML">mzXML (indexed)</option>
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148 <option value="unindexed_mzXML">mzXML (unindexed)</option>
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149 <option value="mgf">mgf</option>
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150 <option value="ms2">ms2</option>
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151 </param>
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152 <conditional name="filtering">
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153 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
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154 <when value="false" />
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155 <when value="true">
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156 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
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157 <!-- BEGIN_VERSION_3 -->
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158 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
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159 <!-- END_VERSION_3 -->
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160
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161
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162 <conditional name="peak_picking">
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163 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
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164 <when value="false" />
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165 <when value="true">
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166 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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167 <option value="1">MS1 Only (1)</option>
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168 <option value="2">MS2 Only (2)</option>
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169 <option value="2-">MS2 and on (2-)</option>
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170 <option value="1-">All Levels (1-)</option>
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171 </param>
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172 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
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173 </when>
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174 </conditional>
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175
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176 <repeat name="threshold_repeat" title="Filter by Threshold">
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177 <conditional name="threshold">
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178 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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179 <option value="count">Peak count</option>
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180 <option value="count-after-ties">Peak count (after ties)</option>
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181 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
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182 <option value="bpi-relative">Percent of base peak intensity</option>
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183 <option value="tic-relative">Percent of total ion current</option>
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184 <option value="tic-fraction">Aggregate percent of total ion current</option>
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185 </param>
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186 <when value="count">
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187 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
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188 </when>
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189 <when value="count-after-ties">
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190 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
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191 </when>
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192 <when value="absolute">
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193 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
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194 </when>
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195 <when value="bpi-relative">
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196 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
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197 />
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198 </when>
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199 <when value="tic-relative">
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200 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
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201 />
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202 </when>
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203 <when value="tic-fraction">
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204 <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" />
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205 </when>
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206 </conditional>
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207 <param type="select" label="Keep" name="orientation">
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208 <option value="most-intense">Most intense peaks</option>
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209 <option value="least-intense">Least intense peaks</option>
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210 </param>
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211 </repeat>
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212
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213
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214 <param name="activation" type="select" label="Filter by Activation">
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215 <option value="false" selected="true">no</option>
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216 <option value="ETD">ETD</option>
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217 <option value="CID">CID</option>
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218 <option value="SA">SA</option>
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219 <option value="HCD">HCD</option>
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220 <!-- BEGIN_VERSION_3 -->
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221 <option>BIRD</option>
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222 <option>ECD</option>
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223 <option>IRMPD</option>
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224 <option>PD</option>
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225 <option>PSD</option>
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226 <option>PQD</option>
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227 <option>SID</option>
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228 <option>SORI</option>
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229 <!-- END_VERSION_3 -->
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230 </param>
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231
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232 <repeat name="indices" title="Filter Scan Indices">
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233 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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234 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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235 </repeat>
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236
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237 <repeat name="scan_numbers" title="Filter Scan Numbers">
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238 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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239 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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240 </repeat>
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241
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242 <conditional name="filter_mz_windows">
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243 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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244 <when value="false" />
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245 <when value="true">
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246 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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247 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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248 </when>
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249 </conditional>
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250
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251 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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252
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253 <conditional name="filter_ms_levels">
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254 <param name="do_filter" type="boolean" label="Filter MS Levels" />
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255 <when value="false" />
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256 <when value="true">
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257 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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258 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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259 </when>
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260 </conditional>
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261
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262 <conditional name="etd_filtering">
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263 <param name="do_etd_filtering" type="select" label="ETD Filtering">
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264 <option value="none" selected="true">none</option>
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265 <option value="default">yes (with default options)</option>
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266 <option value="advanced">yes (show advanced options) </option>
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267 </param>
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268 <when value="none" />
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269 <when value="default" />
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270 <when value="advanced">
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271 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
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272 </param>
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273 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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274 <option value="MZ" selected="true">mz</option>
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275 <option value="PPM">ppm</option>
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276 </param>
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277 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
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278 <option value="true" selected="true">yes</option>
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279 <option value="false">no</option>
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280 </param>
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281 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
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282 <option value="true" selected="true">yes</option>
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283 <option value="false">no</option>
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284 </param>
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285 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
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286 <option value="true" selected="true">yes</option>
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287 <option value="false">no</option>
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288 </param>
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289 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
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290 <option value="true" selected="true">yes</option>
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291 <option value="false">no</option>
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292 </param>
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293 </when>
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294 </conditional>
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295
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296
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297 <!-- BEGIN_VERSION_3 -->
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298 <conditional name="ms2denoise">
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299 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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300 <when value="true">
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301 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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302 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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303 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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304 </when>
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305 <when value="false" />
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306 </conditional>
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307 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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308
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309 <param name="polarity" type="select" label="Filter by Polarity">
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310 <option value="false" selected="true">no</option>
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311 <option value="positive">positive</option>
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312 <option value="negative">negative</option>
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313 </param>
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314
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315 <param name="analyzer" type="select" label="Filter by Analyzer">
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316 <option value="false" selected="true">no</option>
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317 <option value="quad">quad</option>
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318 <option value="orbi">orbi</option>
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319 <option value="FT">FT</option>
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320 <option value="IT">IT</option>
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321 <option value="TOF">TOF</option>
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322 </param>
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323 <!-- END_VERSION_3 -->
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324 </when>
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325 </conditional>
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326
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327 <conditional name="settings">
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328 <param name="settingsType" type="select" label="Advanced Settings" help="">
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329 <option value="default">Use Defaults</option>
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330 <option value="full">Full Parameter List</option>
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331 </param>
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332 <when value="default" />
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333 <when value="full">
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334 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
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335 <option value="64" selected="true">64</option>
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336 <option value="32">32</option>
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337 </param>
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338 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
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339 <option value="64" selected="true">64</option>
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340 <option value="32">32</option>
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341 </param>
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342 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
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343 <option value="64">64</option>
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344 <option value="32" selected="true">32</option>
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345 </param>
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346 <param type="boolean" name="zlib" label="Use zlib">
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347 </param>
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348 </when>
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349 </conditional>
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350
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351
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352 </inputs>
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353 <outputs>
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354 <data format="mzml" name="output">
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355 <change_format>
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356 <when input="output_type" value="mzXML" format="mzxml" />
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357 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
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358 <when input="output_type" value="ms2" format="ms2" />
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359 <when input="output_type" value="mgf" format="mgf" />
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360 </change_format>
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361 </data>
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362 </outputs>
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363
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364 <requirements>
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365 <requirement type="package">proteowizard</requirement>
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366 </requirements>
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367
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368 <help>
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369 **What it does**
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370
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371 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
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372
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373 You can view the original documentation here_.
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374
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375 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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376
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377 ------
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378
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379 **Citation**
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380
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381 For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.`
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382
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383 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
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384
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385 </help>
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386 </tool>
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