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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 #set $ext = $input.ext
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11 #if $ext.startswith("m:")
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12 #set $ext = $ext[len("m:"):]
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13 #end if
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14 msconvert_wrapper.py
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15 --input=${input}
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16 #if hasattr($input, 'display_name')
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17 --input_name='${input.display_name}'
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18 #end if
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19 --output=${output}
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20 ## BEGIN_VERSION_DEFAULT
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21 --fromextension=$ext
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22 ## END_VERSION_DEFAULT
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23
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24 ## BEGIN_VERSION_RAW
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25 --fromextension=RAW
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26 ## END_VERSION_RAW
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27
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28 --toextension=${output_type}
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29
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30 #if $settings.settingsType == "full"
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31 --binaryencoding=${settings.binary_encoding}
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32 --mzencoding=${settings.mz_encoding}
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33 --intensityencoding=${settings.intensity_encoding}
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34 --zlib=${settings.zlib}
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35 #end if
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36
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37 #if $filtering.filtering_use
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38
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39 #if $filtering.precursor_recalculation.value
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40 --filter "precursorRecalculation"
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41 #end if
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42
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43 #if $filtering.peak_picking.pick_peaks
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44 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
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45 #end if
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46
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47 #if str($filtering.activation) != "false"
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48 --filter "activation $filtering.activation"
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49 #end if
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50
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51 #if len($filtering.indices) > 0
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52 --filter "index
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53 #for $index in $filtering.indices
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54 [${index.from},${index.to}]
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55 #end for
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56 "
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57 #end if
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58
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59 #if len($filtering.scan_numbers) > 0
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60 --filter "scanNumber
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61 #for $scan_number in $filtering.scan_numbers
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62 [${scan_number.from},${scan_number.to}]
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63 #end for
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64 "
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65 #end if
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66
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67 #for threshold_entry in $filtering.threshold_repeat
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68 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
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69 #end for
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70
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71
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72 #if $filtering.strip_it.value
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73 --filter "stripIT"
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74 #end if
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75
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76 #if $filtering.filter_mz_windows.do_filter
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77 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
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78 #end if
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79
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80
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81 #if $filtering.filter_ms_levels.do_filter
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82 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
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83 #end if
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84
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85 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
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86 --filter "ETDFilter"
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87 #end if
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88
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89 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
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90 --filter "ETDFilter removePrecursor:$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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91 #end if
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92
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93 ## BEGIN_VERSION_3
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94
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95 #if $filtering.precursor_refine.value
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96 --filter "precursorRefine"
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97 #end if
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98
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99 #if $filtering.ms2denoise.denoise
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100 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
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101 #end if
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102
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103 #if str($filtering.ms2deisotope) == "true"
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104 --filter "MS2Deisotope"
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105 #end if
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106
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107 #if str($filtering.polarity) != "false"
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108 --filter "polarity $filtering.polarity"
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109 #end if
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110
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111 #if str($filtering.analyzer) != "false"
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112 --filter "analyzer $filtering.analyzer"
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113 #end if
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114
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115 ## END_VERSION_3
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116
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117 #end if
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118
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119 </command>
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120
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121 <inputs>
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122 <!-- BEGIN_VERSION_RAW -->
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123 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
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124 <!-- END_VERSION_RAW -->
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125
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126 <!-- BEGIN_VERSION_DEFAULT -->
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127 <conditional name="type">
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128 <param name="input_type" type="select" label="Input Type">
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129 <option value="mzml">mzML</option>
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130 <option value="mzxml">mzXML</option>
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131 <option value="mgf">mgf</option>
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132 <option value="ms2">ms2</option>
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133 </param>
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134 <when value="mzml">
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135 <param format="mzml" name="input" type="data" label="Input mzML"/>
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136 </when>
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137 <when value="mzxml">
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138 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
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139 </when>
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140 <when value="mgf">
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141 <param format="mgf" name="input" type="data" label="Input mgf"/>
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142 </when>
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143 <when value="ms2">
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144 <param format="ms2" name="input" type="data" label="Input ms2"/>
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145 </when>
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146 </conditional>
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147 <!-- END_VERSION_DEFAULT -->
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148 <param name="output_type" type="select" label="Output Type">
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149 <option value="mzML">mzML (indexed)</option>
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150 <option value="unindexed_mzML">mzML (unindexed)</option>
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151 <option value="mzXML">mzXML (indexed)</option>
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152 <option value="unindexed_mzXML">mzXML (unindexed)</option>
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153 <option value="mgf">mgf</option>
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154 <option value="ms2">ms2</option>
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155 </param>
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156 <conditional name="filtering">
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157 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
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158 <when value="false" />
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159 <when value="true">
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160 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
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161 <!-- BEGIN_VERSION_3 -->
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162 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
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163 <!-- END_VERSION_3 -->
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164
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165
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166 <conditional name="peak_picking">
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167 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
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168 <when value="false" />
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169 <when value="true">
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170 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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171 <option value="1">MS1 Only (1)</option>
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172 <option value="2">MS2 Only (2)</option>
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173 <option value="2-">MS2 and on (2-)</option>
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174 <option value="1-">All Levels (1-)</option>
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175 </param>
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176 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
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177 </when>
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178 </conditional>
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179
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180 <repeat name="threshold_repeat" title="Filter by Threshold">
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181 <conditional name="threshold">
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182 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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183 <option value="count">Peak count</option>
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184 <option value="count-after-ties">Peak count (after ties)</option>
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185 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
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186 <option value="bpi-relative">Percent of base peak intensity</option>
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187 <option value="tic-relative">Percent of total ion current</option>
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188 <option value="tic-fraction">Aggregate percent of total ion current</option>
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189 </param>
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190 <when value="count">
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191 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
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192 </when>
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193 <when value="count-after-ties">
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194 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
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195 </when>
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196 <when value="absolute">
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197 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
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198 </when>
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199 <when value="bpi-relative">
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200 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
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201 />
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202 </when>
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203 <when value="tic-relative">
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204 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
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205 />
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206 </when>
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207 <when value="tic-fraction">
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208 <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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209 </when>
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210 </conditional>
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211 <param type="select" label="Keep" name="orientation">
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212 <option value="most-intense">Most intense peaks</option>
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213 <option value="least-intense">Least intense peaks</option>
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214 </param>
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215 </repeat>
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216
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217
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218 <param name="activation" type="select" label="Filter by Activation">
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219 <option value="false" selected="true">no</option>
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220 <option value="ETD">ETD</option>
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221 <option value="CID">CID</option>
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222 <option value="SA">SA</option>
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223 <option value="HCD">HCD</option>
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224 <!-- BEGIN_VERSION_3 -->
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225 <option>BIRD</option>
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226 <option>ECD</option>
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227 <option>IRMPD</option>
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228 <option>PD</option>
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229 <option>PSD</option>
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230 <option>PQD</option>
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231 <option>SID</option>
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232 <option>SORI</option>
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233 <!-- END_VERSION_3 -->
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234 </param>
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235
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236 <repeat name="indices" title="Filter Scan Indices">
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237 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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238 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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239 </repeat>
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240
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241 <repeat name="scan_numbers" title="Filter Scan Numbers">
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242 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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243 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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244 </repeat>
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245
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246 <conditional name="filter_mz_windows">
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247 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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248 <when value="false" />
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249 <when value="true">
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250 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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251 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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252 </when>
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253 </conditional>
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254
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255 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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256
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257 <conditional name="filter_ms_levels">
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258 <param name="do_filter" type="boolean" label="Filter MS Levels" />
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259 <when value="false" />
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260 <when value="true">
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261 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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262 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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263 </when>
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264 </conditional>
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265
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266 <conditional name="etd_filtering">
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267 <param name="do_etd_filtering" type="select" label="ETD Filtering">
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268 <option value="none" selected="true">none</option>
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269 <option value="default">yes (with default options)</option>
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270 <option value="advanced">yes (show advanced options) </option>
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271 </param>
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272 <when value="none" />
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273 <when value="default" />
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274 <when value="advanced">
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275 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
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276 </param>
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277 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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278 <option value="MZ" selected="true">mz</option>
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279 <option value="PPM">ppm</option>
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280 </param>
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281 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
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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_charge_reduced" type="select" label="ETD Remove Charge Reduced">
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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="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
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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 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
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294 <option value="true" selected="true">yes</option>
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295 <option value="false">no</option>
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296 </param>
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297 </when>
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298 </conditional>
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299
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300
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301 <!-- BEGIN_VERSION_3 -->
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302 <conditional name="ms2denoise">
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303 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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304 <when value="true">
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305 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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306 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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307 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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308 </when>
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309 <when value="false" />
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310 </conditional>
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311 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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312
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313 <param name="polarity" type="select" label="Filter by Polarity">
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314 <option value="false" selected="true">no</option>
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315 <option value="positive">positive</option>
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316 <option value="negative">negative</option>
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317 </param>
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318
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319 <param name="analyzer" type="select" label="Filter by Analyzer">
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320 <option value="false" selected="true">no</option>
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321 <option value="quad">quad</option>
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322 <option value="orbi">orbi</option>
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323 <option value="FT">FT</option>
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324 <option value="IT">IT</option>
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325 <option value="TOF">TOF</option>
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326 </param>
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327 <!-- END_VERSION_3 -->
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328 </when>
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329 </conditional>
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330
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331 <conditional name="settings">
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332 <param name="settingsType" type="select" label="Advanced Settings" help="">
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333 <option value="default">Use Defaults</option>
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334 <option value="full">Full Parameter List</option>
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335 </param>
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336 <when value="default" />
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337 <when value="full">
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338 <param type="select" name="binary_encoding" label="Binary 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="mz_encoding" label="m/z Encoding Precision">
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343 <option value="64" selected="true">64</option>
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344 <option value="32">32</option>
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345 </param>
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346 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
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347 <option value="64">64</option>
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348 <option value="32" selected="true">32</option>
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349 </param>
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350 <param type="boolean" name="zlib" label="Use zlib">
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351 </param>
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352 </when>
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353 </conditional>
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354
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355
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356 </inputs>
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357 <outputs>
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358 <data format="mzml" name="output">
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359 <change_format>
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360 <when input="output_type" value="mzXML" format="mzxml" />
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361 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
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362 <when input="output_type" value="ms2" format="ms2" />
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363 <when input="output_type" value="mgf" format="mgf" />
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364 </change_format>
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365 </data>
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366 </outputs>
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367
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368 <requirements>
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369 <requirement type="package">proteowizard</requirement>
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370 <!-- BEGIN_VERSION_RAW -->
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371 <requirement type="platform">windows</requirement>
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372 <!-- END_VERSION_RAW -->
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373 </requirements>
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374
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375 <help>
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376 **What it does**
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377
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378 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
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379
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380 You can view the original documentation here_.
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381
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382 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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383
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384 ------
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385
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386 **Citation**
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387
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388 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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389
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390 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
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391
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392 </help>
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393 </tool>
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