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comparison msconvert_macros.xml @ 6:6b6bba73eadb draft

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planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
author galaxyp
date Tue, 14 Mar 2017 16:52:39 -0400
parents 637e309295cf
children e638f7fad66a
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5:637e309295cf 6:6b6bba73eadb
1 <macros> 1 <macros>
2 <xml name="generic_requirements">
3 <requirements>
4 <requirement type="package" version="3.0.9992">proteowizard</requirement>
5 </requirements>
6 </xml>
7 <token name="@VERSION@">3.0.9992</token>
8
2 <xml name="msconvertCommand"> 9 <xml name="msconvertCommand">
3 <command> 10 <command interpreter="python">
4 <![CDATA[ 11 <![CDATA[
5 #set $output_type_str = str($output_type) 12 #import re
6 #set $input_name = $input.display_name 13 #set $ext = $input.ext
7 #set $output_name = $input_name.split(".")[0] + "." + $output_type_str 14
8 ln -s '$input' '${input_name}' && 15 ## sanitize display name for use as temp filename
9 16 #set basename = 'pwiz_in'
10 #if $data_processing.precursor_refinement.use_mzrefinement 17
11 #set $input_ident_name = $data_processing.precursor_refinement.input_ident.display_name 18 #if hasattr($input, 'display_name')
12 ln -s '${data_processing.precursor_refinement.input_ident}' '${input_ident_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)
13 #end if 22 #end if
14 23
15 mkdir outdir && 24 msconvert_wrapper.py
16 msconvert ${input_name} --$output_type_str -o outdir --outfile '$output_name' 25
26 #if $ext == 'wiff':
27 --input='${input.extra_files_path}/wiff'
28 --input_name='${basename}.wiff'
29 --implicit='${input.extra_files_path}/wiff_scan'
30 --input='${input.extra_files_path}/wiff_scan'
31 --input_name='${basename}.wiff.scan'
32 #else
33 --input='${input}'
34 --input_name='$basename'
35 #end if
36 --output='${output}'
37 ## BEGIN_VERSION_DEFAULT
38 --fromextension=$ext
39 ## END_VERSION_DEFAULT
40 --toextension=${output_type}
17 41
18 ## 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!)
19 #if $data_processing.peak_picking.pick_peaks
20 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
21 #end if
22
23 #if $data_processing.precursor_refinement.use_mzrefinement 43 #if $data_processing.precursor_refinement.use_mzrefinement
44 #set input_ident_name = ".".join(($basename, $data_processing.precursor_refinement.input_ident.ext))
45 --ident='$data_processing.precursor_refinement.input_ident'
46 --ident_name='$input_ident_name'
47 --refinement='$output_refinement'
24 --filter "mzRefiner $input_ident_name 48 --filter "mzRefiner $input_ident_name
25 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels 49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
26 thresholdScore=$data_processing.precursor_refinement.thresholdScore 50 thresholdScore=$data_processing.precursor_refinement.thresholdScore
27 thresholdValue=$data_processing.precursor_refinement.thresholdValue 51 thresholdValue=$data_processing.precursor_refinement.thresholdValue
28 thresholdStep=$data_processing.precursor_refinement.thresholdStep 52 thresholdStep=$data_processing.precursor_refinement.thresholdStep
29 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps" 53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
54 #end if
55
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"
30 #end if 58 #end if
31 59
32 #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"
33 --filter "chargeStatePredictor 61 --filter "chargeStatePredictor
34 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge 62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
46 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge 74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
47 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge" 75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
48 #end if 76 #end if
49 77
50 #for threshold_entry in $data_processing.thresholds 78 #for threshold_entry in $data_processing.thresholds
51 --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"
52 #end for 80 #end for
53 81
54 #if $data_processing.filter_mz_windows.do_mzwindow_filter 82 #if $data_processing.filter_mz_windows.do_mzwindow_filter
55 --filter "mzWindow [$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]"
56 #end if 84 #end if
57 85
58 #if $data_processing.etd_filtering.do_etd_filtering 86 #if $data_processing.etd_filtering.do_etd_filtering
59 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor 87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
60 $data_processing.etd_filtering.remove_charge_reduced 88 $data_processing.etd_filtering.remove_charge_reduced
61 $data_processing.etd_filtering.remove_neutral_loss 89 $data_processing.etd_filtering.remove_neutral_loss
62 $data_processing.etd_filtering.blanket_removal 90 $data_processing.etd_filtering.blanket_removal
63 $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"
64 #end if 92 #end if
65 93
66 #if $data_processing.ms2denoise.denoise 94 #if $data_processing.ms2denoise.denoise
67 --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 $data_processing.ms2denoise.relax"
68 #end if 96 #end if
69 97
70 #if str($data_processing.ms2deisotope) == "true" 98 #if str($data_processing.ms2deisotope) == "true"
71 --filter "MS2Deisotope" 99 --filter "MS2Deisotope"
72 #end if 100 #end if
73 101
74 102
75 ## SCAN INCLUSION/EXCLUSION FILTERS 103 ## SCAN INCLUSION/EXCLUSION FILTERS
76 #if str($filtering.activation) != "false" 104 #if str($filtering.activation) != "false"
77 --filter "activation $filtering.activation" 105 --filter "activation $filtering.activation"
78 #end if 106 #end if
79 107
80 #if len($filtering.indices) > 0 108 #if len($filtering.indices) > 0
81 --filter "index 109 --filter "index
82 #for $index in $filtering.indices 110 #for $index in $filtering.indices
83 [${index.from},${index.to}] 111 [${index.from},${index.to}]
84 #end for 112 #end for
85 " 113 "
86 #end if 114 #end if
87 115
88 #if len($filtering.scan_numbers) > 0 116 #if len($filtering.scan_numbers) > 0
89 --filter "scanNumber 117 --filter "scanNumber
90 #for $scan_number in $filtering.scan_numbers 118 #for $scan_number in $filtering.scan_numbers
91 [${scan_number.from},${scan_number.to}] 119 [${scan_number.from},${scan_number.to}]
92 #end for 120 #end for
93 " 121 "
94 #end if 122 #end if
95 123
96 #if $filtering.strip_it.value 124 #if $filtering.strip_it.value
97 --filter "stripIT" 125 --filter "stripIT"
98 #end if 126 #end if
99 127
100 #if $filtering.filter_ms_levels.do_ms_level_filter 128 #if $filtering.filter_ms_levels.do_ms_level_filter
101 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" 129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
102 #end if 130 #end if
103 131
104 #if str($filtering.polarity) != "false" 132 #if str($filtering.polarity) != "false"
105 --filter "polarity $filtering.polarity" 133 --filter "polarity $filtering.polarity"
106 #end if 134 #end if
107 135
108 #if str($filtering.analyzer) != "false" 136 #if str($filtering.analyzer) != "false"
109 --filter "analyzer $filtering.analyzer" 137 --filter "analyzer $filtering.analyzer"
110 #end if 138 #end if
111 139
112 ## OUTPUT ENCODING 140 ## OUTPUT ENCODING
141 --
113 #set $mz_encoding = str($settings.mz_encoding) 142 #set $mz_encoding = str($settings.mz_encoding)
114 #set $intensity_encoding = str($settings.intensity_encoding) 143 #set $intensity_encoding = str($settings.intensity_encoding)
115 #if $mz_encoding == $intensity_encoding 144 #if $mz_encoding == $intensity_encoding
116 #if $mz_encoding == "64" 145 #if $mz_encoding == "64"
117 --64 146 --64
123 --inten${intensity_encoding} 152 --inten${intensity_encoding}
124 #end if 153 #end if
125 154
126 #set binary_compression = str($settings.binary_compression) 155 #set binary_compression = str($settings.binary_compression)
127 #if $binary_compression == "zlib" 156 #if $binary_compression == "zlib"
128 --zlib 157 --zlib
129 #else if $binary_compression == "numpressLinearPic" 158 #else if $binary_compression == "numpressLinearPic"
130 --numpressLinear --numpressPic 159 --numpressLinear --numpressPic
131 #else if $binary_compression == "numpressLinearSlof" 160 #else if $binary_compression == "numpressLinearSlof"
132 --numpressLinear --numpressSlof 161 --numpressLinear --numpressSlof
133 #else if $binary_compression == "numpressLinear" 162 #else if $binary_compression == "numpressLinear"
134 --numpressLinear 163 --numpressLinear
135 #else if $binary_compression == "numpressPic" 164 #else if $binary_compression == "numpressPic"
136 --numpressPic 165 --numpressPic
137 #else if $binary_compression == "numpressSlof" 166 #else if $binary_compression == "numpressSlof"
138 --numpressSlof 167 --numpressSlof
139 #end if 168 #end if
140 169
141 #if $settings.gzip_compression 170 #if $settings.gzip_compression
142 --gzip 171 --gzip
143 #end if 172 #end if
144 173
145 &&
146
147 #if $data_processing.precursor_refinement.use_mzrefinement
148 mv '${input.name.rsplit('.',1)[0]}.mzRefinement.tsv' output.refinement &&
149 #end if
150
151 mv 'outdir/$output_name' output &&
152 rmdir outdir
153 ]]> 174 ]]>
154 </command> 175 </command>
155 </xml> 176 </xml>
156 177
157 <xml name="msconvertInputParameters"> 178 <xml name="msconvertInputParameters">
185 <conditional name="precursor_refinement"> 206 <conditional name="precursor_refinement">
186 <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" />
187 <when value="false"></when> 208 <when value="false"></when>
188 <when value="true"> 209 <when value="true">
189 <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" />
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+" /> 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+">
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." /> 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>
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)." /> 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)." />
193 <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?" />
194 <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">
195 <option value="1">MS1 Only (1)</option> 226 <option value="1">MS1 Only (1)</option>
196 <option value="2">MS2 Only (2)</option> 227 <option value="2">MS2 Only (2)</option>
299 <option value="false" selected="true">no</option> 330 <option value="false" selected="true">no</option>
300 <option value="ETD">ETD</option> 331 <option value="ETD">ETD</option>
301 <option value="CID">CID</option> 332 <option value="CID">CID</option>
302 <option value="SA">SA</option> 333 <option value="SA">SA</option>
303 <option value="HCD">HCD</option> 334 <option value="HCD">HCD</option>
304 <option>BIRD</option> 335 <option value="BIRD">BIRD</option>
305 <option>ECD</option> 336 <option value="ECD">ECD</option>
306 <option>IRMPD</option> 337 <option value="IRMPD">IRMPD</option>
307 <option>PD</option> 338 <option value="PD">PD</option>
308 <option>PSD</option> 339 <option value="PSD">PSD</option>
309 <option>PQD</option> 340 <option value="PQD">PQD</option>
310 <option>SID</option> 341 <option value="SID">SID</option>
311 <option>SORI</option> 342 <option value="SORI">SORI</option>
312 </param> 343 </param>
313 344
314 <repeat name="indices" title="Filter Scan Indices"> 345 <repeat name="indices" title="Filter Scan Indices">
315 <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" />
316 <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" />
371 </section> 402 </section>
372 </xml> 403 </xml>
373 404
374 <xml name="msconvertOutput"> 405 <xml name="msconvertOutput">
375 <outputs> 406 <outputs>
376 <data format="mzml" name="output" from_work_dir="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" > 407 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
377 <change_format> 408 <change_format>
378 <when input="output_type" value="mz5" format="mz5" /> 409 <when input="output_type" value="mz5" format="mz5" />
379 <when input="output_type" value="mzXML" format="mzxml" /> 410 <when input="output_type" value="mzXML" format="mzxml" />
380 <when input="output_type" value="ms2" format="ms2" /> 411 <when input="output_type" value="ms2" format="ms2" />
381 <when input="output_type" value="mgf" format="mgf" /> 412 <when input="output_type" value="mgf" format="mgf" />
382 </change_format> 413 </change_format>
383 </data> 414 </data>
384 <data format="csv" name="output.refinement" from_work_dir="output.refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv"> 415 <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
385 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> 416 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
386 </data> 417 </data>
387 </outputs> 418 </outputs>
388 </xml> 419 </xml>
420
421
422 <xml name="msconvert_tests">
423 <test>
424 <param name="input" value="small.mzML" />
425 <param name="output_type" value="mzML" />
426 <param name="pick_peaks" value="true" />
427 <param name="pick_peaks_algorithm" value="cwt" />
428 <param name="pick_peaks_ms_levels" value="1-" />
429 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
430 </test>
431
432 <!-- this data file only has profile MS1, so the result is the same -->
433 <test>
434 <param name="input" value="small.mzML" />
435 <param name="output_type" value="mzML" />
436 <param name="pick_peaks" value="true" />
437 <param name="pick_peaks_algorithm" value="cwt" />
438 <param name="pick_peaks_ms_levels" value="1" />
439 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
440 </test>
441 <test>
442 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
443 <param name="output_type" value="mz5" />
444 <param name="mz_encoding" value="64" />
445 <param name="intensity_encoding" value="64" />
446 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" />
447 </test>
448 <test>
449 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
450 <param name="output_type" value="mzXML" />
451 <param name="mz_encoding" value="32" />
452 <param name="intensity_encoding" value="32" />
453 <output name="output" file="small-zlib-32.mzXML" />
454 </test>
455 <!-- TODO: how to test gzipped output?
456 <test>
457 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
458 <param name="output_type" value="mzXML" />
459 <param name="mz_encoding" value="32" />
460 <param name="intensity_encoding" value="32" />
461 <param name="binary_compression" value="false" />
462 <param name="gzip_compression" value="true" />
463 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
464 </test>
465 <test>
466 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
467 <param name="output_type" value="mzML" />
468 <param name="mz_encoding" value="32" />
469 <param name="intensity_encoding" value="32" />
470 <param name="binary_compression" value="false" />
471 <param name="gzip_compression" value="true" />
472 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
473 </test>-->
474
475 <test>
476 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
477 <param name="output_type" value="mzML" />
478 <param name="binary_compression" value="numpressLinearPic" />
479 <output name="output" file="small-numpressLP.mzML" />
480 </test>
481
482 <test>
483 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
484 <param name="output_type" value="mzML" />
485 <param name="binary_compression" value="numpressLinearSlof" />
486 <output name="output" file="small-numpressLS.mzML" />
487 </test>
488
489 <test>
490 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
491 <param name="output_type" value="mzML" />
492 <param name="binary_compression" value="numpressLinear" />
493 <output name="output" file="small-numpressL.mzML" />
494 </test>
495
496 <test>
497 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
498 <param name="output_type" value="mzML" />
499 <param name="binary_compression" value="numpressPic" />
500 <output name="output" file="small-numpressP.mzML" />
501 </test>
502
503 <test>
504 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
505 <param name="output_type" value="mzML" />
506 <param name="binary_compression" value="numpressSlof" />
507 <output name="output" file="small-numpressS.mzML" />
508 </test>
509
510 <test>
511 <param name="input" value="Rpal_01.mz5" />
512 <param name="output_type" value="mzML" />
513 <param name="binary_compression" value="numpressLinearPic" />
514 <param name="use_mzrefinement" value="true" />
515 <param name="input_ident" value="Rpal_01.pepXML" />
516 <param name="thresholdScore" value="mvh" />
517 <param name="thresholdValue" value="40-" />
518 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
519 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
520 </test>
521
522 <test>
523 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
524 <param name="output_type" value="mzML" />
525 <param name="binary_compression" value="numpressLinearPic" />
526 <param name="charge_state_calculation_method" value="predictor" />
527 <param name="predictor_overrideExistingCharge" value="true" />
528 <param name="minMultipleCharge" value="2" />
529 <param name="maxMultipleCharge" value="5" />
530 <param name="singleChargeFractionTIC" value="0.95" />
531 <param name="maxKnownCharge" value="8" />
532 <output name="output" file="small-chargeStatePredictor.mzML" />
533 </test>
534 <test>
535 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
536 <param name="output_type" value="mzML" />
537 <param name="binary_compression" value="numpressLinearPic" />
538 <param name="charge_state_calculation_method" value="turbocharger" />
539 <param name="minCharge" value="1" />
540 <param name="maxCharge" value="5" />
541 <param name="precursorsBefore" value="1" />
542 <param name="precursorsAfter" value="1" />
543 <param name="halfIsoWidth" value="1.5" />
544 <param name="defaultMinCharge" value="1" />
545 <param name="defaultMaxCharge" value="5" />
546 <output name="output" file="small-turbocharger.mzML" />
547 </test>
548 <test>
549 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
550 <param name="output_type" value="mzML" />
551 <param name="do_etd_filtering" value="true" />
552 <param name="remove_precursor" value="true" />
553 <param name="remove_charge_reduced" value="true" />
554 <param name="remove_neutral_loss" value="false" />
555 <param name="blanket_removal" value="false" />
556 <param name="matching_tolerance" value="50" />
557 <param name="matching_tolerance_units" value="ppm" />
558 <param name="binary_compression" value="numpressLinearPic" />
559 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
560 </test>
561 <test>
562 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
563 <param name="output_type" value="mzML" />
564 <param name="thresholds_0|threshold_type" value="count" />
565 <param name="thresholds_0|value" value="100" />
566 <param name="thresholds_0|orientation" value="most-intense" />
567 <param name="thresholds_1|threshold_type" value="absolute" />
568 <param name="thresholds_1|value" value="1" />
569 <param name="thresholds_1|orientation" value="most-intense" />
570 <param name="binary_compression" value="numpressLinearPic" />
571 <output name="output" file="small-threshold.mzML" />
572 </test>
573 <test>
574 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
575 <param name="output_type" value="mzML" />
576 <param name="do_mzwindow_filter" value="true" />
577 <param name="mz_window_from" value="420" />
578 <param name="mz_window_to" value="840" />
579 <param name="binary_compression" value="numpressLinearPic" />
580 <output name="output" file="small-mzWindow.mzML" />
581 </test>
582 <test>
583 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
584 <param name="output_type" value="mzML" />
585 <param name="denoise" value="true" />
586 <param name="num_peaks" value="10" />
587 <param name="window_width" value="40" />
588 <param name="relax" value="false" />
589 <param name="binary_compression" value="numpressLinearPic" />
590 <output name="output" file="small-denoise.mzML" />
591 </test>
592 <test>
593 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
594 <param name="output_type" value="mzML" />
595 <param name="ms2deisotope" value="true" />
596 <param name="binary_compression" value="numpressLinearPic" />
597 <output name="output" file="small-deisotope.mzML" />
598 </test>
599 <test>
600 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
601 <param name="output_type" value="mzML" />
602 <param name="activation" value="CID" />
603 <param name="binary_compression" value="numpressLinearPic" />
604 <output name="output" file="small-activation.mzML" />
605 </test>
606 <test>
607 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
608 <param name="output_type" value="mzML" />
609 <param name="indices_0|from" value="2" />
610 <param name="indices_0|to" value="4" />
611 <param name="indices_1|from" value="10" />
612 <param name="indices_1|to" value="10" />
613 <param name="indices_2|from" value="13" />
614 <param name="indices_2|to" value="15" />
615 <param name="binary_compression" value="numpressLinearPic" />
616 <output name="output" file="small-index-filter.mzML" />
617 </test>
618 <test>
619 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
620 <param name="output_type" value="mzML" />
621 <param name="strip_it" value="true" />
622 <param name="binary_compression" value="numpressLinearPic" />
623 <output name="output" file="small-strip-it.mzML" />
624 </test>
625 <test>
626 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
627 <param name="output_type" value="mzML" />
628 <param name="do_ms_level_filter" value="true" />
629 <param name="ms_level_from" value="2" />
630 <param name="ms_level_to" value="2" />
631 <param name="binary_compression" value="numpressLinearPic" />
632 <output name="output" file="small-ms-level-filter.mzML" />
633 </test>
634 <test>
635 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
636 <param name="output_type" value="mzML" />
637 <param name="polarity" value="positive" />
638 <param name="binary_compression" value="numpressLinearPic" />
639 <output name="output" file="small-polarity-filter.mzML" />
640 </test>
641 <test>
642 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
643 <param name="output_type" value="mzML" />
644 <param name="analyzer" value="IT" />
645 <param name="binary_compression" value="numpressLinearPic" />
646 <output name="output" file="small-analyzer-filter.mzML" />
647 </test>
648 <test>
649 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
650 <param name="output_type" value="mzML" />
651 <param name="scan_numbers_0|from" value="3" />
652 <param name="scan_numbers_0|to" value="5" />
653 <param name="scan_numbers_1|from" value="11" />
654 <param name="scan_numbers_1|to" value="11" />
655 <param name="scan_numbers_2|from" value="14" />
656 <param name="scan_numbers_2|to" value="16" />
657 <param name="binary_compression" value="numpressLinearPic" />
658 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
659 </test>
660 <!--<test>
661 <param name="input" value="small.mzML" />
662 <param name="output_type" value="mzML" />
663 <param name="binary_compression" value="numpressLinearPic" />
664 <output name="output" file="small-deisotope-poisson.mzML" />
665 </test>-->
666 </xml>
667 <xml name="msconvert_help">
668 **What it does**
669
670 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
671
672 You can view the original documentation here_.
673
674 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
675 </xml>
676
677 <xml name="citations">
678 <citations>
679 <citation type="doi">10.1093/bioinformatics/btn323</citation>
680 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
681 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
682 </citations>
683 </xml>
684
389 </macros> 685 </macros>