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comparison msconvert_macros.xml @ 1:7016f1f10f42 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
author galaxyp
date Tue, 14 Mar 2017 16:45:30 -0400
parents baa6c072fccc
children
comparison
equal deleted inserted replaced
0:baa6c072fccc 1:7016f1f10f42
1 <macros> 1 <macros>
2 <xml name="generic_requirements"> 2 <xml name="generic_requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.0.9016">proteowizard</requirement> 4 <requirement type="package" version="3.0.9992">proteowizard</requirement>
5 </requirements> 5 </requirements>
6 </xml> 6 </xml>
7 <token name="@VERSION@">3.0</token> 7 <token name="@VERSION@">3.0.9992</token>
8 8
9 <xml name="msconvertCommand"> 9 <xml name="msconvertCommand">
10 <command interpreter="python"> 10 <command interpreter="python">
11 <![CDATA[ 11 <![CDATA[
12 #import re 12 #import re
13 #set $ext = $input.ext 13 #set $ext = $input.ext
14
15 ## sanitize display name for use as temp filename
16 #set basename = 'pwiz_in'
17
18 #if hasattr($input, 'display_name')
19 ## explicit inclusion or exclusion ??
20 #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.display_name)
21 ##set basename = $re.sub(r'[\/\\\;\|\&\>\<]','_',$input.display_name)
22 #end if
23
14 msconvert_wrapper.py 24 msconvert_wrapper.py
25
15 #if $ext == 'wiff': 26 #if $ext == 'wiff':
16 #set basename = 'absciex' 27 --input='${input.extra_files_path}/wiff'
17 #if hasattr($input, 'display_name') 28 --input_name='${basename}.wiff'
18 #set basename = $re.sub('\W','_',$input.display_name) 29 --implicit='${input.extra_files_path}/wiff_scan'
19 #end if 30 --input='${input.extra_files_path}/wiff_scan'
20 --input=${input.extra_files_path}/wiff 31 --input_name='${basename}.wiff.scan'
21 --input_name='${basename}.wiff
22 --implicit=${input.extra_files_path}/wiff_scan
23 --input=${input.extra_files_path}/wiff_scan
24 --input_name='${basename}.wiff.scan
25 #else 32 #else
26 --input=${input} 33 --input='${input}'
27 #if hasattr($input, 'display_name') 34 --input_name='$basename'
28 --input_name='${input.display_name}'
29 #end if
30 #end if 35 #end if
31 --output=${output} 36 --output='${output}'
32 ## BEGIN_VERSION_DEFAULT 37 ## BEGIN_VERSION_DEFAULT
33 --fromextension=$ext 38 --fromextension=$ext
34 ## END_VERSION_DEFAULT 39 ## END_VERSION_DEFAULT
35 --toextension=${output_type} 40 --toextension=${output_type}
36 41
37 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) 42 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
38 #if $data_processing.precursor_refinement.use_mzrefinement 43 #if $data_processing.precursor_refinement.use_mzrefinement
39 #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name) 44 #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))
40 #if $data_processing.precursor_refinement.input_ident.ext == 'mzid': 45 --ident='$data_processing.precursor_refinement.input_ident'
41 #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name) 46 --ident_name='$input_ident_name'
42 #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml': 47 --refinement='$output_refinement'
43 #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name)
44 #end if
45 --ident=$data_processing.precursor_refinement.input_ident
46 --ident_name=$input_ident_name
47 --refinement=$output_refinement
48 --filter "mzRefiner $input_ident_name 48 --filter "mzRefiner $input_ident_name
49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels 49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
50 thresholdScore=$data_processing.precursor_refinement.thresholdScore 50 thresholdScore=$data_processing.precursor_refinement.thresholdScore
51 thresholdValue=$data_processing.precursor_refinement.thresholdValue 51 thresholdValue=$data_processing.precursor_refinement.thresholdValue
52 thresholdStep=$data_processing.precursor_refinement.thresholdStep 52 thresholdStep=$data_processing.precursor_refinement.thresholdStep
53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps" 53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
54 #end if 54 #end if
55 55
56 #if $data_processing.peak_picking.pick_peaks 56 #if $data_processing.peak_picking.pick_peaks
57 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" 57 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
58 #end if 58 #end if
59 59
60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor" 60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
61 --filter "chargeStatePredictor 61 --filter "chargeStatePredictor
62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge 62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge 74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge" 75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
76 #end if 76 #end if
77 77
78 #for threshold_entry in $data_processing.thresholds 78 #for threshold_entry in $data_processing.thresholds
79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" 79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
80 #end for 80 #end for
81 81
82 #if $data_processing.filter_mz_windows.do_mzwindow_filter 82 #if $data_processing.filter_mz_windows.do_mzwindow_filter
83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" 83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
84 #end if 84 #end if
85 85
86 #if $data_processing.etd_filtering.do_etd_filtering 86 #if $data_processing.etd_filtering.do_etd_filtering
87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor 87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
88 $data_processing.etd_filtering.remove_charge_reduced 88 $data_processing.etd_filtering.remove_charge_reduced
89 $data_processing.etd_filtering.remove_neutral_loss 89 $data_processing.etd_filtering.remove_neutral_loss
90 $data_processing.etd_filtering.blanket_removal 90 $data_processing.etd_filtering.blanket_removal
91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units" 91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
92 #end if 92 #end if
93 93
94 #if $data_processing.ms2denoise.denoise 94 #if $data_processing.ms2denoise.denoise
95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" 95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
96 #end if 96 #end if
97 97
98 #if str($data_processing.ms2deisotope) == "true" 98 #if str($data_processing.ms2deisotope) == "true"
99 --filter "MS2Deisotope" 99 --filter "MS2Deisotope"
100 #end if 100 #end if
101 101
102 102
103 ## SCAN INCLUSION/EXCLUSION FILTERS 103 ## SCAN INCLUSION/EXCLUSION FILTERS
104 #if str($filtering.activation) != "false" 104 #if str($filtering.activation) != "false"
105 --filter "activation $filtering.activation" 105 --filter "activation $filtering.activation"
106 #end if 106 #end if
107 107
108 #if len($filtering.indices) > 0 108 #if len($filtering.indices) > 0
109 --filter "index 109 --filter "index
110 #for $index in $filtering.indices 110 #for $index in $filtering.indices
111 [${index.from},${index.to}] 111 [${index.from},${index.to}]
112 #end for 112 #end for
113 " 113 "
114 #end if 114 #end if
115 115
116 #if len($filtering.scan_numbers) > 0 116 #if len($filtering.scan_numbers) > 0
117 --filter "scanNumber 117 --filter "scanNumber
118 #for $scan_number in $filtering.scan_numbers 118 #for $scan_number in $filtering.scan_numbers
119 [${scan_number.from},${scan_number.to}] 119 [${scan_number.from},${scan_number.to}]
120 #end for 120 #end for
121 " 121 "
122 #end if 122 #end if
123 123
124 #if $filtering.strip_it.value 124 #if $filtering.strip_it.value
125 --filter "stripIT" 125 --filter "stripIT"
126 #end if 126 #end if
127 127
128 #if $filtering.filter_ms_levels.do_ms_level_filter 128 #if $filtering.filter_ms_levels.do_ms_level_filter
129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" 129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
130 #end if 130 #end if
131 131
132 #if str($filtering.polarity) != "false" 132 #if str($filtering.polarity) != "false"
133 --filter "polarity $filtering.polarity" 133 --filter "polarity $filtering.polarity"
134 #end if 134 #end if
135 135
136 #if str($filtering.analyzer) != "false" 136 #if str($filtering.analyzer) != "false"
137 --filter "analyzer $filtering.analyzer" 137 --filter "analyzer $filtering.analyzer"
138 #end if 138 #end if
139 139
140 ## OUTPUT ENCODING 140 ## OUTPUT ENCODING
141 -- 141 --
142 #set $mz_encoding = str($settings.mz_encoding) 142 #set $mz_encoding = str($settings.mz_encoding)
152 --inten${intensity_encoding} 152 --inten${intensity_encoding}
153 #end if 153 #end if
154 154
155 #set binary_compression = str($settings.binary_compression) 155 #set binary_compression = str($settings.binary_compression)
156 #if $binary_compression == "zlib" 156 #if $binary_compression == "zlib"
157 --zlib 157 --zlib
158 #else if $binary_compression == "numpressLinearPic" 158 #else if $binary_compression == "numpressLinearPic"
159 --numpressLinear --numpressPic 159 --numpressLinear --numpressPic
160 #else if $binary_compression == "numpressLinearSlof" 160 #else if $binary_compression == "numpressLinearSlof"
161 --numpressLinear --numpressSlof 161 --numpressLinear --numpressSlof
162 #else if $binary_compression == "numpressLinear" 162 #else if $binary_compression == "numpressLinear"
163 --numpressLinear 163 --numpressLinear
164 #else if $binary_compression == "numpressPic" 164 #else if $binary_compression == "numpressPic"
165 --numpressPic 165 --numpressPic
166 #else if $binary_compression == "numpressSlof" 166 #else if $binary_compression == "numpressSlof"
167 --numpressSlof 167 --numpressSlof
168 #end if 168 #end if
169 169
170 #if $settings.gzip_compression 170 #if $settings.gzip_compression
171 --gzip 171 --gzip
172 #end if 172 #end if
173 173
174 ]]> 174 ]]>
175 </command> 175 </command>
176 </xml> 176 </xml>
201 <option value="cwt">CantWaiT - continuous wavelet transform</option> 201 <option value="cwt">CantWaiT - continuous wavelet transform</option>
202 </param> 202 </param>
203 </when> 203 </when>
204 </conditional> 204 </conditional>
205 205
206 <conditional name="precursor_refinement" title="MZRefinery Precursor Refinement" expanded="true"> 206 <conditional name="precursor_refinement">
207 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" /> 207 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
208 <when value="false"></when> 208 <when value="false"></when>
209 <when value="true"> 209 <when value="true">
210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" /> 210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
211 <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+" /> 211 <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+">
212 <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." /> 212 <sanitizer>
213 <valid initial="string.letters" />
214 </sanitizer>
215 </param>
216 <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.">
217 <sanitizer>
218 <valid initial="string.letters,string.digits">
219 <add value="-" />
220 </valid>
221 </sanitizer>
222 </param>
213 <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)." /> 223 <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)." />
214 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" /> 224 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
215 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels"> 225 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
216 <option value="1">MS1 Only (1)</option> 226 <option value="1">MS1 Only (1)</option>
217 <option value="2">MS2 Only (2)</option> 227 <option value="2">MS2 Only (2)</option>
320 <option value="false" selected="true">no</option> 330 <option value="false" selected="true">no</option>
321 <option value="ETD">ETD</option> 331 <option value="ETD">ETD</option>
322 <option value="CID">CID</option> 332 <option value="CID">CID</option>
323 <option value="SA">SA</option> 333 <option value="SA">SA</option>
324 <option value="HCD">HCD</option> 334 <option value="HCD">HCD</option>
325 <option>BIRD</option> 335 <option value="BIRD">BIRD</option>
326 <option>ECD</option> 336 <option value="ECD">ECD</option>
327 <option>IRMPD</option> 337 <option value="IRMPD">IRMPD</option>
328 <option>PD</option> 338 <option value="PD">PD</option>
329 <option>PSD</option> 339 <option value="PSD">PSD</option>
330 <option>PQD</option> 340 <option value="PQD">PQD</option>
331 <option>SID</option> 341 <option value="SID">SID</option>
332 <option>SORI</option> 342 <option value="SORI">SORI</option>
333 </param> 343 </param>
334 344
335 <repeat name="indices" title="Filter Scan Indices"> 345 <repeat name="indices" title="Filter Scan Indices">
336 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> 346 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
337 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> 347 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
431 <test> 441 <test>
432 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 442 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
433 <param name="output_type" value="mz5" /> 443 <param name="output_type" value="mz5" />
434 <param name="mz_encoding" value="64" /> 444 <param name="mz_encoding" value="64" />
435 <param name="intensity_encoding" value="64" /> 445 <param name="intensity_encoding" value="64" />
436 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" /> 446 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
437 </test> 447 </test>
438 <test> 448 <test>
439 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 449 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
440 <param name="output_type" value="mzXML" /> 450 <param name="output_type" value="mzXML" />
441 <param name="mz_encoding" value="32" /> 451 <param name="mz_encoding" value="32" />
500 <test> 510 <test>
501 <param name="input" value="Rpal_01.mz5" /> 511 <param name="input" value="Rpal_01.mz5" />
502 <param name="output_type" value="mzML" /> 512 <param name="output_type" value="mzML" />
503 <param name="binary_compression" value="numpressLinearPic" /> 513 <param name="binary_compression" value="numpressLinearPic" />
504 <param name="use_mzrefinement" value="true" /> 514 <param name="use_mzrefinement" value="true" />
505 <param name="input_ident" value="Rpal_01.pepXML.gz" /> 515 <param name="input_ident" value="Rpal_01.pepXML" />
506 <param name="thresholdScore" value="mvh" /> 516 <param name="thresholdScore" value="mvh" />
507 <param name="thresholdValue" value="40-" /> 517 <param name="thresholdValue" value="40-" />
508 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> 518 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
509 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> 519 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
510 </test> 520 </test>
511 521
512 <test> 522 <test>
513 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> 523 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
514 <param name="output_type" value="mzML" /> 524 <param name="output_type" value="mzML" />