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annotate msconvert.xml @ 4:158a71ee5733 draft

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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 17:43:19 -0500
parents 8e2e7ff2b6bd
children 637e309295cf
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1 <tool id="msconvert" name="msconvert" version="0.3.0">
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2 <!-- BEGIN_VERSION_DEFAULT -->
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3 <description>Convert and filter a mass spec peak list</description>
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4 <!-- END_VERSION_DEFAULT -->
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5 <!--
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6 <requirements>
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7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
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8 </requirements>
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9 -->
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10 <command interpreter="python">
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11 #import re
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12 #set $ext = $input.ext
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13 msconvert_wrapper.py
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14 #if $type.input_type == 'wiff':
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15 #set basename = 'absciex'
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16 #if hasattr($input, 'display_name')
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17 #set basename = $re.sub('\W','_',$input.display_name)
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18 #end if
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19 --input=${input.extra_files_path}/wiff
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20 --input_name='${basename}.wiff
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21 --implicit=${input.extra_files_path}/wiff_scan
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22 --input=${input.extra_files_path}/wiff_scan
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23 --input_name='${basename}.wiff.scan
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24 #else
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25 --input=${input}
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26 #if hasattr($input, 'display_name')
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27 --input_name='${input.display_name}'
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28 #end if
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29 #end if
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30 --output=${output}
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31 ## BEGIN_VERSION_DEFAULT
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32 --fromextension=$ext
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33 ## END_VERSION_DEFAULT
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36 --toextension=${output_type}
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37
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38 #if $settings.settingsType == "full"
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39 --binaryencoding=${settings.binary_encoding}
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40 --mzencoding=${settings.mz_encoding}
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41 --intensityencoding=${settings.intensity_encoding}
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42 --zlib=${settings.zlib}
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43 #end if
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45 #if $filtering.filtering_use
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46
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47 #if $filtering.precursor_recalculation.value
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48 --filter "precursorRecalculation"
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49 #end if
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50
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51 #if $filtering.peak_picking.pick_peaks
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52 --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels"
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53 #end if
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54
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55 #if str($filtering.activation) != "false"
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56 --filter "activation $filtering.activation"
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57 #end if
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58
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59 #if len($filtering.indices) > 0
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60 --filter "index
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61 #for $index in $filtering.indices
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62 [${index.from},${index.to}]
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63 #end for
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64 "
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65 #end if
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66
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67 #if len($filtering.scan_numbers) > 0
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68 --filter "scanNumber
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69 #for $scan_number in $filtering.scan_numbers
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70 [${scan_number.from},${scan_number.to}]
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71 #end for
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72 "
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73 #end if
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74
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75 #for threshold_entry in $filtering.threshold_repeat
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76 --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation"
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77 #end for
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78
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79
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80 #if $filtering.strip_it.value
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81 --filter "stripIT"
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82 #end if
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83
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84 #if $filtering.filter_mz_windows.do_filter
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85 --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]"
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86 #end if
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87
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88
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89 #if $filtering.filter_ms_levels.do_filter
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90 --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]"
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91 #end if
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92
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93 #if str($filtering.etd_filtering.do_etd_filtering) == "default"
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94 --filter "ETDFilter"
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95 #end if
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96
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97 #if str($filtering.etd_filtering.do_etd_filtering) == "advanced"
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98 --filter "ETDFilter removePrecursor:$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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99 #end if
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100
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101 ## BEGIN_VERSION_3
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102
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103 #if $filtering.precursor_refine.value
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104 --filter "precursorRefine"
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105 #end if
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106
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107 #if $filtering.ms2denoise.denoise
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108 --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax"
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109 #end if
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110
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111 #if str($filtering.ms2deisotope) == "true"
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112 --filter "MS2Deisotope"
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113 #end if
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114
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115 #if str($filtering.polarity) != "false"
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116 --filter "polarity $filtering.polarity"
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117 #end if
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118
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119 #if str($filtering.analyzer) != "false"
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120 --filter "analyzer $filtering.analyzer"
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121 #end if
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122
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123 ## END_VERSION_3
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124
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125 #end if
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126
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127 </command>
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128
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129 <inputs>
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130
4
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131 <!-- BEGIN_VERSION_DEFAULT -->
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132 <conditional name="type">
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133 <param name="input_type" type="select" label="Input Type">
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134 <option value="mzml">mzML</option>
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135 <option value="mzxml">mzXML</option>
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136 <option value="mgf">mgf</option>
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137 <option value="ms2">ms2</option>
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138 <option value="wiff">wiff</option>
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139 </param>
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140 <when value="mzml">
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141 <param format="mzml" name="input" type="data" label="Input mzML"/>
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142 </when>
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143 <when value="mzxml">
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144 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
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145 </when>
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146 <when value="mgf">
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147 <param format="mgf" name="input" type="data" label="Input mgf"/>
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148 </when>
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149 <when value="ms2">
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150 <param format="ms2" name="input" type="data" label="Input ms2"/>
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151 </when>
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152 <when value="wiff">
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153 <param format="wiff" name="input" type="data" label="Input wiff"/>
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154 </when>
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155 </conditional>
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156 <!-- END_VERSION_DEFAULT -->
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157 <param name="output_type" type="select" label="Output Type">
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158 <option value="mzML">mzML (indexed)</option>
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159 <option value="unindexed_mzML">mzML (unindexed)</option>
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160 <option value="mzXML">mzXML (indexed)</option>
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161 <option value="unindexed_mzXML">mzXML (unindexed)</option>
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162 <option value="mgf">mgf</option>
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163 <option value="ms2">ms2</option>
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164 </param>
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165 <conditional name="filtering">
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166 <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
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167 <when value="false" />
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168 <when value="true">
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169 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
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170 <!-- BEGIN_VERSION_3 -->
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171 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
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172 <!-- END_VERSION_3 -->
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173
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174
4
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175 <conditional name="peak_picking">
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176 <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" />
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177 <when value="false" />
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178 <when value="true">
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179 <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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180 <option value="1">MS1 Only (1)</option>
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181 <option value="2">MS2 Only (2)</option>
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182 <option value="2-">MS2 and on (2-)</option>
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183 <option value="1-">All Levels (1-)</option>
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184 </param>
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185 <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/>
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186 </when>
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187 </conditional>
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188
4
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189 <repeat name="threshold_repeat" title="Filter by Threshold">
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190 <conditional name="threshold">
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191 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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192 <option value="count">Peak count</option>
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193 <option value="count-after-ties">Peak count (after ties)</option>
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194 <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z -->
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195 <option value="bpi-relative">Percent of base peak intensity</option>
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196 <option value="tic-relative">Percent of total ion current</option>
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197 <option value="tic-fraction">Aggregate percent of total ion current</option>
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198 </param>
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199 <when value="count">
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200 <param type="integer" name="value" label="Number of peaks to keep" value="100" />
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201 </when>
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202 <when value="count-after-ties">
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203 <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" />
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204 </when>
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205 <when value="absolute">
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206 <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" />
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207 </when>
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208 <when value="bpi-relative">
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209 <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2"
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210 />
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211 </when>
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212 <when value="tic-relative">
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213 <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2"
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214 />
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215 </when>
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216 <when value="tic-fraction">
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217 <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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218 </when>
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219 </conditional>
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220 <param type="select" label="Keep" name="orientation">
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221 <option value="most-intense">Most intense peaks</option>
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222 <option value="least-intense">Least intense peaks</option>
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223 </param>
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224 </repeat>
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225
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226
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227 <param name="activation" type="select" label="Filter by Activation">
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228 <option value="false" selected="true">no</option>
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229 <option value="ETD">ETD</option>
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230 <option value="CID">CID</option>
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231 <option value="SA">SA</option>
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232 <option value="HCD">HCD</option>
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233 <!-- BEGIN_VERSION_3 -->
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234 <option>BIRD</option>
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235 <option>ECD</option>
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236 <option>IRMPD</option>
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237 <option>PD</option>
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238 <option>PSD</option>
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239 <option>PQD</option>
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240 <option>SID</option>
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241 <option>SORI</option>
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242 <!-- END_VERSION_3 -->
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243 </param>
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244
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245 <repeat name="indices" title="Filter Scan Indices">
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246 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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247 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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248 </repeat>
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249
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250 <repeat name="scan_numbers" title="Filter Scan Numbers">
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251 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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252 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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253 </repeat>
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254
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255 <conditional name="filter_mz_windows">
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256 <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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257 <when value="false" />
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258 <when value="true">
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259 <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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260 <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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261 </when>
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262 </conditional>
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263
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264 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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265
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266 <conditional name="filter_ms_levels">
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267 <param name="do_filter" type="boolean" label="Filter MS Levels" />
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268 <when value="false" />
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269 <when value="true">
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270 <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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271 <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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272 </when>
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273 </conditional>
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274
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275 <conditional name="etd_filtering">
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276 <param name="do_etd_filtering" type="select" label="ETD Filtering">
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277 <option value="none" selected="true">none</option>
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278 <option value="default">yes (with default options)</option>
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279 <option value="advanced">yes (show advanced options) </option>
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280 </param>
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281 <when value="none" />
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282 <when value="default" />
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283 <when value="advanced">
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284 <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1">
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285 </param>
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286 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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287 <option value="MZ" selected="true">mz</option>
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288 <option value="PPM">ppm</option>
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289 </param>
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290 <param name="remove_precursor" type="select" label="ETD Remove Precursor">
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291 <option value="true" selected="true">yes</option>
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292 <option value="false">no</option>
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293 </param>
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294 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced">
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295 <option value="true" selected="true">yes</option>
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296 <option value="false">no</option>
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297 </param>
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298 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss">
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299 <option value="true" selected="true">yes</option>
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300 <option value="false">no</option>
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301 </param>
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302 <param name="blanket_removal" type="select" label="ETD Blanket Removal">
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303 <option value="true" selected="true">yes</option>
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304 <option value="false">no</option>
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305 </param>
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306 </when>
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307 </conditional>
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308
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309
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310 <!-- BEGIN_VERSION_3 -->
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311 <conditional name="ms2denoise">
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312 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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313 <when value="true">
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314 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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315 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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316 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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317 </when>
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318 <when value="false" />
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319 </conditional>
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320 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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321
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322 <param name="polarity" type="select" label="Filter by Polarity">
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323 <option value="false" selected="true">no</option>
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324 <option value="positive">positive</option>
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325 <option value="negative">negative</option>
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326 </param>
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327
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328 <param name="analyzer" type="select" label="Filter by Analyzer">
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329 <option value="false" selected="true">no</option>
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330 <option value="quad">quad</option>
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331 <option value="orbi">orbi</option>
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332 <option value="FT">FT</option>
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333 <option value="IT">IT</option>
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334 <option value="TOF">TOF</option>
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335 </param>
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336 <!-- END_VERSION_3 -->
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337 </when>
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338 </conditional>
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339
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340 <conditional name="settings">
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341 <param name="settingsType" type="select" label="Advanced Settings" help="">
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342 <option value="default">Use Defaults</option>
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343 <option value="full">Full Parameter List</option>
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344 </param>
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345 <when value="default" />
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346 <when value="full">
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347 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
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348 <option value="64" selected="true">64</option>
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349 <option value="32">32</option>
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350 </param>
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351 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
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352 <option value="64" selected="true">64</option>
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353 <option value="32">32</option>
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354 </param>
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355 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
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356 <option value="64">64</option>
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357 <option value="32" selected="true">32</option>
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358 </param>
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359 <param type="boolean" name="zlib" label="Use zlib">
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360 </param>
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361 </when>
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362 </conditional>
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363
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364
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365 </inputs>
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366 <outputs>
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367 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" >
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368 <change_format>
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369 <when input="output_type" value="mzXML" format="mzxml" />
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370 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
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371 <when input="output_type" value="ms2" format="ms2" />
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372 <when input="output_type" value="mgf" format="mgf" />
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373 </change_format>
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374 </data>
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375 </outputs>
0
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376 <help>
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377 **What it does**
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378
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379 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
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380
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381 You can view the original documentation here_.
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382
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383 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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384
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385 ------
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386
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387 **Citation**
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388
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389 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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390
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391 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/msconvert
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392
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393 </help>
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394 </tool>