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annotate msconvert_raw.xml @ 2:8e2e7ff2b6bd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit 815179cfd9754d3859239258fa30c331d5daaa41-dirty
author galaxyp
date Thu, 22 Oct 2015 17:41:29 -0400
parents ab59b1826345
children 158a71ee5733
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1 <tool id="msconvert_raw" name="msconvert (vendor support)" version="0.3.0">
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2 <description>Convert and/or filter mass spectrometry files (with vendor support on Windows)</description>
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4 <requirements>
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5 <requirement type="package" version="3.0.9016">proteowizard</requirement>
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6 </requirements>
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8 <macros>
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9 <import>msconvert_macros.xml</import>
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10 </macros>
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12 <expand macro="msconvertCommand" />
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14 <inputs>
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15 <!-- TODO: add Bruker, Waters, Agilent types -->
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16 <param format="mzml,mzxml,mz5,mgf,wiff,raw" name="input" type="data" label="Input unrefined MS data" />
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18 <expand macro="msconvertInputParameters" />
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19 </inputs>
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21 <expand macro="msconvertOutput" />
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23 <tests>
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24 <test>
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25 <param name="input" value="small.mzML" />
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26 <param name="output_type" value="mzML" />
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27 <param name="pick_peaks" value="true" />
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28 <param name="pick_peaks_algorithm" value="cwt" />
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29 <param name="pick_peaks_ms_levels" value="1-" />
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30 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
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31 </test>
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33 <!-- this data file only has profile MS1, so the result is the same -->
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34 <test>
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35 <param name="input" value="small.mzML" />
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36 <param name="output_type" value="mzML" />
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37 <param name="pick_peaks" value="true" />
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38 <param name="pick_peaks_algorithm" value="cwt" />
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39 <param name="pick_peaks_ms_levels" value="1" />
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40 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
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41 </test>
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42 <test>
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43 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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44 <param name="output_type" value="mz5" />
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45 <param name="mz_encoding" value="64" />
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46 <param name="intensity_encoding" value="64" />
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47 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
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48 </test>
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49 <test>
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50 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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51 <param name="output_type" value="mzXML" />
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52 <param name="mz_encoding" value="32" />
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53 <param name="intensity_encoding" value="32" />
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54 <output name="output" file="small-zlib-32.mzXML" />
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55 </test>
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56 <!-- TODO: how to test gzipped output?
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57 <test>
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58 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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59 <param name="output_type" value="mzXML" />
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60 <param name="mz_encoding" value="32" />
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61 <param name="intensity_encoding" value="32" />
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62 <param name="binary_compression" value="false" />
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63 <param name="gzip_compression" value="true" />
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64 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
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65 </test>
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66 <test>
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67 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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68 <param name="output_type" value="mzML" />
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69 <param name="mz_encoding" value="32" />
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70 <param name="intensity_encoding" value="32" />
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71 <param name="binary_compression" value="false" />
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72 <param name="gzip_compression" value="true" />
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73 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
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74 </test>-->
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76 <test>
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77 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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78 <param name="output_type" value="mzML" />
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79 <param name="binary_compression" value="numpressLinearPic" />
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80 <output name="output" file="small-numpressLP.mzML" />
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81 </test>
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83 <test>
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84 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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85 <param name="output_type" value="mzML" />
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86 <param name="binary_compression" value="numpressLinearSlof" />
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87 <output name="output" file="small-numpressLS.mzML" />
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88 </test>
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90 <test>
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91 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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92 <param name="output_type" value="mzML" />
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93 <param name="binary_compression" value="numpressLinear" />
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94 <output name="output" file="small-numpressL.mzML" />
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95 </test>
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96
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97 <test>
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98 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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99 <param name="output_type" value="mzML" />
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100 <param name="binary_compression" value="numpressPic" />
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101 <output name="output" file="small-numpressP.mzML" />
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102 </test>
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103
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104 <test>
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105 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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106 <param name="output_type" value="mzML" />
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107 <param name="binary_compression" value="numpressSlof" />
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108 <output name="output" file="small-numpressS.mzML" />
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109 </test>
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110
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111 <test>
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112 <param name="input" value="Rpal_01.mz5" />
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113 <param name="output_type" value="mzML" />
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114 <param name="binary_compression" value="numpressLinearPic" />
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115 <param name="use_mzrefinement" value="true" />
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116 <param name="input_ident" value="Rpal_01.pepXML.gz" />
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117 <param name="thresholdScore" value="mvh" />
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118 <param name="thresholdValue" value="40-" />
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119 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
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120 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
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121 </test>
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122
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123 <test>
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124 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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125 <param name="output_type" value="mzML" />
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126 <param name="binary_compression" value="numpressLinearPic" />
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127 <param name="charge_state_calculation_method" value="predictor" />
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128 <param name="predictor_overrideExistingCharge" value="true" />
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129 <param name="minMultipleCharge" value="2" />
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130 <param name="maxMultipleCharge" value="5" />
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131 <param name="singleChargeFractionTIC" value="0.95" />
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132 <param name="maxKnownCharge" value="8" />
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133 <output name="output" file="small-chargeStatePredictor.mzML" />
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134 </test>
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135 <test>
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136 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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137 <param name="output_type" value="mzML" />
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138 <param name="binary_compression" value="numpressLinearPic" />
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139 <param name="charge_state_calculation_method" value="turbocharger" />
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140 <param name="minCharge" value="1" />
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141 <param name="maxCharge" value="5" />
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142 <param name="precursorsBefore" value="1" />
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143 <param name="precursorsAfter" value="1" />
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144 <param name="halfIsoWidth" value="1.5" />
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145 <param name="defaultMinCharge" value="1" />
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146 <param name="defaultMaxCharge" value="5" />
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147 <output name="output" file="small-turbocharger.mzML" />
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148 </test>
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149 <test>
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150 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
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151 <param name="output_type" value="mzML" />
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152 <param name="do_etd_filtering" value="true" />
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153 <param name="remove_precursor" value="true" />
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154 <param name="remove_charge_reduced" value="true" />
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155 <param name="remove_neutral_loss" value="false" />
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156 <param name="blanket_removal" value="false" />
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157 <param name="matching_tolerance" value="50" />
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158 <param name="matching_tolerance_units" value="ppm" />
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159 <param name="binary_compression" value="numpressLinearPic" />
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160 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
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161 </test>
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162 <test>
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163 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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164 <param name="output_type" value="mzML" />
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165 <param name="thresholds_0|threshold_type" value="count" />
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166 <param name="thresholds_0|value" value="100" />
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167 <param name="thresholds_0|orientation" value="most-intense" />
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168 <param name="thresholds_1|threshold_type" value="absolute" />
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169 <param name="thresholds_1|value" value="1" />
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170 <param name="thresholds_1|orientation" value="most-intense" />
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171 <param name="binary_compression" value="numpressLinearPic" />
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172 <output name="output" file="small-threshold.mzML" />
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173 </test>
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174 <test>
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175 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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176 <param name="output_type" value="mzML" />
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177 <param name="do_mzwindow_filter" value="true" />
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178 <param name="mz_window_from" value="420" />
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179 <param name="mz_window_to" value="840" />
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180 <param name="binary_compression" value="numpressLinearPic" />
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181 <output name="output" file="small-mzWindow.mzML" />
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182 </test>
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183 <test>
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184 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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185 <param name="output_type" value="mzML" />
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186 <param name="denoise" value="true" />
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187 <param name="num_peaks" value="10" />
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188 <param name="window_width" value="40" />
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189 <param name="relax" value="false" />
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190 <param name="binary_compression" value="numpressLinearPic" />
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191 <output name="output" file="small-denoise.mzML" />
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192 </test>
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193 <test>
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194 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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195 <param name="output_type" value="mzML" />
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196 <param name="ms2deisotope" value="true" />
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197 <param name="binary_compression" value="numpressLinearPic" />
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198 <output name="output" file="small-deisotope.mzML" />
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199 </test>
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200 <test>
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201 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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202 <param name="output_type" value="mzML" />
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203 <param name="activation" value="CID" />
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204 <param name="binary_compression" value="numpressLinearPic" />
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205 <output name="output" file="small-activation.mzML" />
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206 </test>
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207 <test>
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208 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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209 <param name="output_type" value="mzML" />
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210 <param name="indices_0|from" value="2" />
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211 <param name="indices_0|to" value="4" />
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212 <param name="indices_1|from" value="10" />
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213 <param name="indices_1|to" value="10" />
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214 <param name="indices_2|from" value="13" />
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215 <param name="indices_2|to" value="15" />
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216 <param name="binary_compression" value="numpressLinearPic" />
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217 <output name="output" file="small-index-filter.mzML" />
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218 </test>
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219 <test>
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220 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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221 <param name="output_type" value="mzML" />
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222 <param name="strip_it" value="true" />
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223 <param name="binary_compression" value="numpressLinearPic" />
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224 <output name="output" file="small-strip-it.mzML" />
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225 </test>
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226 <test>
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227 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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228 <param name="output_type" value="mzML" />
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229 <param name="do_ms_level_filter" value="true" />
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230 <param name="ms_level_from" value="2" />
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231 <param name="ms_level_to" value="2" />
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232 <param name="binary_compression" value="numpressLinearPic" />
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233 <output name="output" file="small-ms-level-filter.mzML" />
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234 </test>
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235 <test>
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236 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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237 <param name="output_type" value="mzML" />
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238 <param name="polarity" value="positive" />
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239 <param name="binary_compression" value="numpressLinearPic" />
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240 <output name="output" file="small-polarity-filter.mzML" />
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241 </test>
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242 <test>
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243 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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244 <param name="output_type" value="mzML" />
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245 <param name="analyzer" value="IT" />
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246 <param name="binary_compression" value="numpressLinearPic" />
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247 <output name="output" file="small-analyzer-filter.mzML" />
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248 </test>
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249 <test>
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250 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
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251 <param name="output_type" value="mzML" />
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252 <param name="scan_numbers_0|from" value="3" />
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253 <param name="scan_numbers_0|to" value="5" />
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254 <param name="scan_numbers_1|from" value="11" />
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255 <param name="scan_numbers_1|to" value="11" />
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256 <param name="scan_numbers_2|from" value="14" />
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257 <param name="scan_numbers_2|to" value="16" />
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258 <param name="binary_compression" value="numpressLinearPic" />
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259 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
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260 </test>
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261 <!--<test>
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262 <param name="input" value="small.mzML" />
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263 <param name="output_type" value="mzML" />
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264 <param name="binary_compression" value="numpressLinearPic" />
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265 <output name="output" file="small-deisotope-poisson.mzML" />
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266 </test>-->
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267 </tests>
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268 <help>
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269 **What it does**
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270
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271 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
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272
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273 You can view the original documentation here_.
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274
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275 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
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276 </help>
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277 <citations>
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278 <citation type="doi">10.1093/bioinformatics/btn323</citation>
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279 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
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280 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
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281 </citations>
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282 </tool>