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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=${input}
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12 --output=${output}
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13 ## BEGIN_VERSION_DEFAULT
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14 --fromextension=${input.ext}
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15 ## END_VERSION_DEFAULT
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16
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17 ## BEGIN_VERSION_RAW
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18 --fromextension=RAW
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19 ## END_VERSION_RAW
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20
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21 --toextension=${output_type}
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22
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23 #if $settings.settingsType == "full"
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24 --binaryencoding=${settings.binary_encoding}
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25 --mzencoding=${settings.mz_encoding}
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26 --intensityencoding=${settings.intensity_encoding}
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27 --zlib=${settings.zlib}
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28 #end if
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29
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30 #if $filtering.filtering_use
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31
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32 #if $filtering.precursor_recalculation.value
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33 --filter "precursorRecalculation"
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34 #end if
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35
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36 #if $filtering.peak_picking.pick_peaks
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37 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
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38 #end if
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39
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40 #if str($filtering.activation) != "false"
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41 --filter "activation $filtering.activation"
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42 #end if
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43
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44 #if len($filtering.indices) > 0
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45 --filter "index
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46 #for $index in $filtering.indices
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47 [${index.from},${index.to}]
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48 #end for
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49 "
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50 #end if
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51
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52 #if len($filtering.scan_numbers) > 0
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53 --filter "scanNumber
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54 #for $scanNumber in $filtering.scanNumbers
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55 [${scanNumber.from},${scanNumber.to}]
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56 #end for
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57 "
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58 #end if
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59
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60 #if $filtering.strip_it.value
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61 --filter "stripIT"
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62 #end if
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63
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64 #if $filtering.filter_mz_windows.do_filter
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65 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
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66 #end if
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67
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68
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69 #if $filtering.filter_ms_levels.do_filter
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70 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
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71 #end if
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72
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73 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
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74 --filter "ETDFilter"
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75 #end if
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76
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77 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
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78 --filter "ETDFilter removePrecursor:$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 $filtering.etd_filtering.matching_tolerance_units"
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79 #end if
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80
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81 ## BEGIN_VERSION_3
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82 #if str($filtering.ms2deisotope) == "true"
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83 --filter "MS2Deisotope"
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84 #end if
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85
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86 #if str($filtering.polarity) != "false"
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87 --filter "polarity $filtering.polarity"
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88 #end if
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89
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90 #if str($filtering.analyzer) != "false"
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91 --filter "analyzer $filtering.analyzer"
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92 #end if
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93
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94 ## END_VERSION_3
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95
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96 #end if
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97
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98 </command>
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99
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100 <inputs>
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101 <!-- BEGIN_VERSION_RAW -->
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102 <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/>
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103 <!-- END_VERSION_RAW -->
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104
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105 <!-- BEGIN_VERSION_DEFAULT -->
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106 <conditional name="type">
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107 <param name="input_type" type="select" label="Input Type">
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108 <option value="mzml">mzML</option>
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109 <option value="mzxml">mzXML</option>
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110 <option value="mgf">mgf</option>
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111 <option value="ms2">ms2</option>
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112 </param>
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113 <when value="mzml">
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114 <param format="mzml" name="input" type="data" label="Input mzML"/>
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115 </when>
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116 <when value="mzxml">
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117 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
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118 </when>
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119 <when value="mgf">
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120 <param format="mgf" name="input" type="data" label="Input mgf"/>
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121 </when>
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122 <when value="ms2">
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123 <param format="ms2" name="input" type="data" label="Input ms2"/>
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124 </when>
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125 </conditional>
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126 <!-- END_VERSION_DEFAULT -->
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127 <param name="output_type" type="select" label="Output Type">
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128 <option value="mzML">mzML (indexed)</option>
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129 <option value="unindexed_mzML">mzML (unindexed)</option>
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130 <option value="mzXML">mzXML (indexed)</option>
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131 <option value="unindexed_mzXML">mzXML (unindexed)</option>
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132 <option value="mgf">mgf</option>
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133 <option value="ms2">ms2</option>
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134 </param>
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135 <conditional name="filtering">
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136 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" />
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137 <when value="false" />
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138 <when value="true">
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139 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
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140
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141 <conditional name="peak_picking">
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142 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
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143 <when value="false" />
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144 <when value="true">
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145 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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146 <option value="1">MS1 Only (1)</option>
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147 <option value="2">MS2 Only (2)</option>
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148 <option value="2-">MS2 and on (2-)</option>
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149 <option value="1-">All Levels (1-)</option>
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150 </param>
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151 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
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152 </when>
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153 </conditional>
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154
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155
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156 <param name="activation" type="select" label="Filter by Activation">
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157 <option value="false" selected="true">no</option>
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158 <option value="ETD">ETD</option>
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159 <option value="CID">CID</option>
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160 <option value="SA">SA</option>
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161 <option value="HCD">HCD</option>
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162 <!-- BEGIN_VERSION_3 -->
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163 <option>BIRD</option>
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164 <option>ECD</option>
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165 <option>IRMPD</option>
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166 <option>PD</option>
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167 <option>PSD</option>
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168 <option>PQD</option>
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169 <option>SID</option>
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170 <option>SORI</option>
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171 <!-- END_VERSION_3 -->
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172 </param>
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173
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174 <repeat name="indices" title="Filter Scan Indices">
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175 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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176 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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177 </repeat>
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178
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179 <repeat name="scan_numbers" title="Filter Scan Numbers">
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180 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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181 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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182 </repeat>
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183
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184 <conditional name="filter_mz_windows">
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185 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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186 <when value="false" />
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187 <when value="true">
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188 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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189 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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190 </when>
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191 </conditional>
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192
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193
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194 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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195
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196 <conditional name="filter_ms_levels">
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197 <param name="do_filter" type="boolean" label="Filter MS Levels" />
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198 <when value="false" />
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199 <when value="true">
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200 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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201 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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202 </when>
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203 </conditional>
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204
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205 <conditional name="etd_filtering">
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206 <param name="do_etd_filtering" type="select" label="ETD Filtering">
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207 <option value="none" selected="true">none</option>
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208 <option value="default">yes (with default options)</option>
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209 <option value="advanced">yes (show advanced options) </option>
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210 </param>
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211 <when value="none" />
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212 <when value="default" />
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213 <when value="advanced">
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214 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
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215 </param>
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216 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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217 <option value="MZ" selected="true">mz</option>
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218 <option value="PPM">ppm</option>
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219 </param>
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220 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
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221 <option value="true" selected="true">yes</option>
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222 <option value="false">no</option>
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223 </param>
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224 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
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225 <option value="true" selected="true">yes</option>
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226 <option value="false">no</option>
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227 </param>
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228 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
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229 <option value="true" selected="true">yes</option>
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230 <option value="false">no</option>
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231 </param>
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232 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
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233 <option value="true" selected="true">yes</option>
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234 <option value="false">no</option>
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235 </param>
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236 </when>
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237 </conditional>
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238
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239
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240 <!-- BEGIN_VERSION_3 -->
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241 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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242
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243 <param name="polarity" type="select" label="Filter by Polarity">
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244 <option value="false" selected="true">no</option>
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245 <option value="positive">positive</option>
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246 <option value="negative">negative</option>
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247 </param>
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248
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249 <param name="analyzer" type="select" label="Filter by Analyzer">
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250 <option value="false" selected="true">no</option>
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251 <option value="quad">quad</option>
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252 <option value="orbi">orbi</option>
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253 <option value="FT">FT</option>
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254 <option value="IT">IT</option>
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255 <option value="TOF">TOF</option>
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256 </param>
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257 <!-- END_VERSION_3 -->
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258 </when>
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259 </conditional>
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260
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261 <conditional name="settings">
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262 <param name="settingsType" type="select" label="Advanced Settings" help="">
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263 <option value="default">Use Defaults</option>
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264 <option value="full">Full Parameter List</option>
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265 </param>
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266 <when value="default" />
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267 <when value="full">
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268 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
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269 <option value="64" selected="true">64</option>
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270 <option value="32">32</option>
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271 </param>
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272 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
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273 <option value="64" selected="true">64</option>
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274 <option value="32">32</option>
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275 </param>
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276 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
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277 <option value="64">64</option>
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278 <option value="32" selected="true">32</option>
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279 </param>
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280 <param type="boolean" name="zlib" label="Use zlib">
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281 </param>
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282 </when>
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283 </conditional>
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284
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285
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286 </inputs>
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287 <outputs>
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288 <data format="mzml" name="output">
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289 <change_format>
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290 <when input="output_type" value="mzxml" format="mzxml" />
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291 <when input="output_type" value="unindexed_mzxml" format="mzxml" />
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292 <when input="output_type" value="ms2" format="ms2" />
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293 <when input="output_type" value="mgf" format="mgf" />
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294 </change_format>
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295 </data>
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296 </outputs>
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297
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298 <requirements>
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299 <requirement type="package">proteowizard</requirement>
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300 </requirements>
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301
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302 <help>
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303 **What it does**
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304
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305 Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available.
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306
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307 You can view the original documentation here_.
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308
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309 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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310
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311 ------
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312
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313 **Citation**
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314
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315 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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316
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317 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert
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318
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319 </help>
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320 </tool>
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