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annotate msconvert_macros.xml @ 5:637e309295cf draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
author galaxyp
date Mon, 12 Dec 2016 17:07:11 -0500
parents 158a71ee5733
children 6b6bba73eadb
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1 <macros>
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2 <xml name="msconvertCommand">
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637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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3 <command>
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4 <![CDATA[
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637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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5 #set $output_type_str = str($output_type)
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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6 #set $input_name = $input.display_name
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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7 #set $output_name = $input_name.split(".")[0] + "." + $output_type_str
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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8 ln -s '$input' '${input_name}' &&
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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10 #if $data_processing.precursor_refinement.use_mzrefinement
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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11 #set $input_ident_name = $data_processing.precursor_refinement.input_ident.display_name
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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12 ln -s '${data_processing.precursor_refinement.input_ident}' '${input_ident_name}' &&
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13 #end if
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637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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15 mkdir outdir &&
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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16 msconvert ${input_name} --$output_type_str -o outdir --outfile '$output_name'
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18 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
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19 #if $data_processing.peak_picking.pick_peaks
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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20 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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21 #end if
637e309295cf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/msconvert commit d70aeb6f0e03a354fb8732f04dce8453b03477ea
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22
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23 #if $data_processing.precursor_refinement.use_mzrefinement
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24 --filter "mzRefiner $input_ident_name
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25 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
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26 thresholdScore=$data_processing.precursor_refinement.thresholdScore
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27 thresholdValue=$data_processing.precursor_refinement.thresholdValue
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28 thresholdStep=$data_processing.precursor_refinement.thresholdStep
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29 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
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30 #end if
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31
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32 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
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33 --filter "chargeStatePredictor
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34 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
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35 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
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36 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
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37 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
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38 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
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39 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
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40 --filter "turbocharger
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41 minCharge=$data_processing.charge_state_calculation.minCharge
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42 maxCharge=$data_processing.charge_state_calculation.maxCharge
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43 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
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44 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
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45 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
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46 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
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47 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
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48 #end if
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49
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50 #for threshold_entry in $data_processing.thresholds
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51 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
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52 #end for
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53
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54 #if $data_processing.filter_mz_windows.do_mzwindow_filter
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55 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
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56 #end if
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57
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58 #if $data_processing.etd_filtering.do_etd_filtering
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59 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
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60 $data_processing.etd_filtering.remove_charge_reduced
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61 $data_processing.etd_filtering.remove_neutral_loss
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62 $data_processing.etd_filtering.blanket_removal
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63 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
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64 #end if
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65
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66 #if $data_processing.ms2denoise.denoise
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67 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
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68 #end if
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69
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70 #if str($data_processing.ms2deisotope) == "true"
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71 --filter "MS2Deisotope"
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72 #end if
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74
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75 ## SCAN INCLUSION/EXCLUSION FILTERS
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76 #if str($filtering.activation) != "false"
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77 --filter "activation $filtering.activation"
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78 #end if
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79
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80 #if len($filtering.indices) > 0
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81 --filter "index
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82 #for $index in $filtering.indices
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83 [${index.from},${index.to}]
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84 #end for
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85 "
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86 #end if
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87
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88 #if len($filtering.scan_numbers) > 0
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89 --filter "scanNumber
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90 #for $scan_number in $filtering.scan_numbers
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91 [${scan_number.from},${scan_number.to}]
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92 #end for
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93 "
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94 #end if
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95
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96 #if $filtering.strip_it.value
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97 --filter "stripIT"
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98 #end if
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99
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100 #if $filtering.filter_ms_levels.do_ms_level_filter
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101 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
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102 #end if
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103
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104 #if str($filtering.polarity) != "false"
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105 --filter "polarity $filtering.polarity"
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106 #end if
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107
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108 #if str($filtering.analyzer) != "false"
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109 --filter "analyzer $filtering.analyzer"
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110 #end if
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111
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112 ## OUTPUT ENCODING
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113 #set $mz_encoding = str($settings.mz_encoding)
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114 #set $intensity_encoding = str($settings.intensity_encoding)
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115 #if $mz_encoding == $intensity_encoding
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116 #if $mz_encoding == "64"
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117 --64
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118 #else
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119 --32
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120 #end if
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121 #else
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122 --mz${mz_encoding}
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123 --inten${intensity_encoding}
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124 #end if
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125
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126 #set binary_compression = str($settings.binary_compression)
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127 #if $binary_compression == "zlib"
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128 --zlib
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129 #else if $binary_compression == "numpressLinearPic"
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130 --numpressLinear --numpressPic
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131 #else if $binary_compression == "numpressLinearSlof"
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132 --numpressLinear --numpressSlof
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133 #else if $binary_compression == "numpressLinear"
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134 --numpressLinear
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135 #else if $binary_compression == "numpressPic"
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136 --numpressPic
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137 #else if $binary_compression == "numpressSlof"
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138 --numpressSlof
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139 #end if
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140
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141 #if $settings.gzip_compression
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142 --gzip
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143 #end if
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144
5
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145 &&
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146
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147 #if $data_processing.precursor_refinement.use_mzrefinement
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148 mv '${input.name.rsplit('.',1)[0]}.mzRefinement.tsv' output.refinement &&
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149 #end if
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150
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151 mv 'outdir/$output_name' output &&
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152 rmdir outdir
4
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153 ]]>
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154 </command>
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155 </xml>
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156
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157 <xml name="msconvertInputParameters">
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158 <param name="output_type" type="select" label="Output Type">
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159 <option value="mz5" selected="true">mz5</option>
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160 <option value="mzML">mzML</option>
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161 <option value="mzXML">mzXML</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
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166 <section name="data_processing" title="Data Processing Filters">
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167
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168 <conditional name="peak_picking">
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169 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
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170 <when value="false" />
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171 <when value="true">
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172 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
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173 <option value="1">MS1 Only (1)</option>
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174 <option value="2">MS2 Only (2)</option>
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175 <option value="2-">MS2 and on (2-)</option>
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176 <option value="1-" selected="true">All Levels (1-)</option>
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177 </param>
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178 <param type="select" name="pick_peaks_algorithm" label="Peak Picking - Algorithm" help="The vendor method only works on Agilent, Bruker, Sciex, Thermo data, and only on Windows (although some vendors work on Wine)">
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179 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
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180 <option value="cwt">CantWaiT - continuous wavelet transform</option>
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181 </param>
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182 </when>
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183 </conditional>
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184
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185 <conditional name="precursor_refinement">
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186 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
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187 <when value="false"></when>
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188 <when value="true">
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189 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
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190 <param name="thresholdScore" type="text" value="mvh" label="MZRefinery - Threshold Score Name" help="E.g. 'mvh' for MyriMatch, 'xcorr' for Sequest, 'specevalue' for MS-GF+" />
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191 <param name="thresholdValue" type="text" value="50-" label="MZRefinery - Threshold Score Value" help="MZRefinery uses peptide-spectrum-matches with scores from this range to build its model. '100-' means score equal to or greater than 100. '-1e-10' means less than or equal to 1e-10." />
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192 <param name="thresholdStep" type="float" value="0" label="MZRefinery - Threshold Score Step" help="If there are not enough quality hits at the given score threshold value, the threshold can be increased by this step (until maxSteps is reached)." />
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193 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
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194 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
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195 <option value="1">MS1 Only (1)</option>
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196 <option value="2">MS2 Only (2)</option>
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197 <option value="2-">MS2 and on (2-)</option>
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198 <option value="1-" selected="true">All Levels (1-)</option>
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199 </param>
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200 </when>
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201 </conditional>
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202
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203 <conditional name="charge_state_calculation">
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204 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
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205 <option value="false">no</option>
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206 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
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207 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
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208 </param>
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209 <when value="false" />
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210 <when value="predictor">
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211 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
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212 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
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213 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
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214 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
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215 <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for &quot;known&quot; charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
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216 </when>
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217 <when value="turbocharger">
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218 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
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219 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
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220 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
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221 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
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222 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
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223 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
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224 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
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225 </when>
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226 </conditional>
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227
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228 <repeat name="thresholds" title="Filter by Threshold">
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229 <param type="select" label="Specify threshold on" name="threshold_type" help="">
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230 <option value="count">Peak count</option>
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231 <option value="count-after-ties">Peak count (after ties)</option>
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232 <option value="absolute">Peak absolute intensity</option>
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233 <option value="bpi-relative">Fraction of base peak intensity</option>
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234 <option value="tic-relative">Fraction of total ion current</option>
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235 <option value="tic-fraction">Aggregate fraction of total ion current</option>
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236 </param>
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237 <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the &quot;Aggregated fraction&quot; method, peaks are accepted until this fraction of the TIC is accounted for." />
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238 <param type="select" label="Keep" name="orientation">
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239 <option value="most-intense">Most intense peaks</option>
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240 <option value="least-intense">Least intense peaks</option>
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241 </param>
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242 </repeat>
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243
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244 <conditional name="filter_mz_windows">
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245 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
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246 <when value="false" />
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247 <when value="true">
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248 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
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249 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
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250 </when>
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251 </conditional>
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252
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253 <conditional name="etd_filtering">
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254 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
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255 <when value="false" />
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256 <when value="true">
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257 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
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258 <option value="true" selected="true">yes</option>
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259 <option value="false">no</option>
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260 </param>
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261 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
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262 <option value="true" selected="true">yes</option>
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263 <option value="false">no</option>
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264 </param>
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265 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
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266 <option value="true" selected="true">yes</option>
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267 <option value="false">no</option>
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268 </param>
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269 <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
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270 <option value="true" selected="true">yes</option>
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271 <option value="false">no</option>
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272 </param>
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273 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
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274 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
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275 <option value="MZ" selected="true">mz</option>
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276 <option value="PPM">ppm</option>
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277 </param>
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278 </when>
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279 </conditional>
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280
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281 <conditional name="ms2denoise">
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282 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
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283 <when value="true">
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284 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
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285 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
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286 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
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287 </when>
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288 <when value="false" />
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289 </conditional>
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290
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291 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
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292
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293 </section>
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294
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295
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296 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
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297
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298 <param name="activation" type="select" label="Filter by Activation">
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299 <option value="false" selected="true">no</option>
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300 <option value="ETD">ETD</option>
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301 <option value="CID">CID</option>
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302 <option value="SA">SA</option>
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303 <option value="HCD">HCD</option>
5
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304 <option>BIRD</option>
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305 <option>ECD</option>
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306 <option>IRMPD</option>
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307 <option>PD</option>
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308 <option>PSD</option>
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309 <option>PQD</option>
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310 <option>SID</option>
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311 <option>SORI</option>
4
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312 </param>
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313
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314 <repeat name="indices" title="Filter Scan Indices">
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315 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
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316 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
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317 </repeat>
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318
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319 <repeat name="scan_numbers" title="Filter Scan Numbers">
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320 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
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321 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
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322 </repeat>
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323
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324 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
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325
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326 <conditional name="filter_ms_levels">
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327 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
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328 <when value="false" />
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329 <when value="true">
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330 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
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331 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
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332 </when>
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333 </conditional>
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334
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335 <param name="polarity" type="select" label="Filter by Polarity">
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336 <option value="false" selected="true">no</option>
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337 <option value="positive">positive</option>
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338 <option value="negative">negative</option>
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339 </param>
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340
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341 <param name="analyzer" type="select" label="Filter by Analyzer">
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342 <option value="false" selected="true">no</option>
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343 <option value="quad">Quadrupole</option>
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344 <option value="orbi">Orbitrap</option>
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345 <option value="FT">Fourier-transform</option>
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346 <option value="IT">Ion trap</option>
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347 <option value="TOF">Time of flight</option>
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348 </param>
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349 </section>
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350
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351
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352 <section name="settings" title="Output Encoding Settings">
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353 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
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354 <option value="64" selected="true">64</option>
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355 <option value="32">32</option>
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356 </param>
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357 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
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358 <option value="64">64</option>
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359 <option value="32" selected="true">32</option>
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360 </param>
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361 <param type="select" name="binary_compression" label="Binary data compression">
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362 <option value="false">None</option>
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363 <option value="zlib" selected="true">zlib</option>
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364 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
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365 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
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366 <option value="numpressLinear">numpressLinear only</option>
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367 <option value="numpressPic">numpressPic only</option>
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368 <option value="numpressSlof">numpressSlof only</option>
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369 </param>
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370 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
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371 </section>
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372 </xml>
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373
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374 <xml name="msconvertOutput">
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375 <outputs>
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376 <data format="mzml" name="output" from_work_dir="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
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377 <change_format>
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378 <when input="output_type" value="mz5" format="mz5" />
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379 <when input="output_type" value="mzXML" format="mzxml" />
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380 <when input="output_type" value="ms2" format="ms2" />
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381 <when input="output_type" value="mgf" format="mgf" />
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382 </change_format>
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383 </data>
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384 <data format="csv" name="output.refinement" from_work_dir="output.refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
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385 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
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386 </data>
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387 </outputs>
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388 </xml>
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389 </macros>