Mercurial > repos > galaxyp > msconvert
comparison msconvert_macros.xml @ 10:9d5de24e6ef7 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d595e3cfe190a61d81005f9be7c2652aa5f91292
author | galaxyp |
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date | Sat, 23 Feb 2019 06:25:48 -0500 |
parents | dd4ba10d0c45 |
children | cc5ccfa8ee28 |
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9:dd4ba10d0c45 | 10:9d5de24e6ef7 |
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1 <macros> | 1 <macros> |
2 <xml name="generic_requirements"> | 2 <token name="@VERSION@">3.0.19052</token> |
3 <requirements> | 3 <token name="@FULL_VERSION@">@VERSION@-089e81090</token> |
4 <requirement type="package" version="3.0.9016">proteowizard</requirement> | |
5 </requirements> | |
6 </xml> | |
7 <token name="@VERSION@">3.0</token> | |
8 | 4 |
9 <xml name="msconvertCommand"> | 5 <xml name="msconvertCommand"> |
10 <command interpreter="python"> | 6 <command detect_errors="exit_code"> |
11 <![CDATA[ | 7 <![CDATA[ |
12 #import re | 8 #import re |
13 #set $ext = $input.ext | 9 #set $ext = $input.ext |
14 msconvert_wrapper.py | 10 |
11 ## sanitize display name for use as temp filename | |
12 #set basename = $re.sub(r'[^\w\.\-\+]','_',$input.element_identifier) | |
13 | |
15 #if $ext == 'wiff': | 14 #if $ext == 'wiff': |
16 #set basename = 'absciex' | 15 ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' && |
17 #if hasattr($input, 'display_name') | 16 ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' && |
18 #set basename = $re.sub('\W','_',$input.display_name) | 17 #elif $ext.endswith('tar'): |
19 #end if | 18 ln -s '$input' '${basename}' && |
20 --input=${input.extra_files_path}/wiff | 19 tar xf '${basename}' && |
21 --input_name='${basename}.wiff | 20 #set basename = $os.path.splitext($basename)[0] |
22 --implicit=${input.extra_files_path}/wiff_scan | |
23 --input=${input.extra_files_path}/wiff_scan | |
24 --input_name='${basename}.wiff.scan | |
25 #else | 21 #else |
26 --input=${input} | 22 ln -s '$input' '${basename}' && |
27 #if hasattr($input, 'display_name') | |
28 --input_name='${input.display_name}' | |
29 #end if | |
30 #end if | 23 #end if |
31 --output=${output} | 24 |
32 ## BEGIN_VERSION_DEFAULT | 25 #if $data_processing.precursor_refinement.use_mzrefinement |
33 --fromextension=$ext | 26 #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext)) |
34 ## END_VERSION_DEFAULT | 27 #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv' |
35 --toextension=${output_type} | 28 ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' && |
29 #end if | |
30 | |
31 uid=`id -u` && | |
32 gid=`id -g` && | |
33 | |
34 wine64_anyuser msconvert '${basename}' | |
35 --outdir outputs | |
36 --${output_type} | |
37 | |
38 #if $general_options.combineIonMobilitySpectra: | |
39 --combineIonMobilitySpectra | |
40 #end if | |
41 | |
42 #if $general_options.simAsSpectra: | |
43 --simAsSpectra | |
44 #end if | |
45 | |
46 #if $general_options.srmAsSpectra: | |
47 --srmAsSpectra | |
48 #end if | |
49 | |
50 #if $general_options.acceptZeroLengthSpectra: | |
51 --acceptZeroLengthSpectra | |
52 #end if | |
53 | |
54 #if $general_options.ignoreUnknownInstrumentError: | |
55 --ignoreUnknownInstrumentError | |
56 #end if | |
57 | |
58 #if $general_options.scan_summing.do_scan_summing: | |
59 --filter "scanSumming precursorTol=$general_options.scan_summing.precursorTol scanTimeTol=$general_options.scan_summing.scanTimeTol ionMobilityTol=$general_options.scan_summing.ionMobilityTol" | |
60 #end if | |
61 | |
62 #if $general_options.multi_run_output.do_multi_run_output: | |
63 #if len($general_options.multi_run_output.run_index_set) > 0 | |
64 --runIndexSet " | |
65 #for $index in $general_options.multi_run_output.run_index_set | |
66 [${index.from},${index.to}] | |
67 #end for | |
68 " | |
69 #end if | |
70 #else | |
71 --runIndexSet $general_options.multi_run_output.runIndexSet | |
72 #end if | |
73 | |
74 ## Strip sourceFile location since it is meaningless on HPC systems and causes problems with functional tests | |
75 --stripLocationFromSourceFiles | |
36 | 76 |
37 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) | 77 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!) |
78 #if $data_processing.peak_picking.pick_peaks | |
79 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels" | |
80 #end if | |
81 | |
38 #if $data_processing.precursor_refinement.use_mzrefinement | 82 #if $data_processing.precursor_refinement.use_mzrefinement |
39 #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name) | |
40 #if $data_processing.precursor_refinement.input_ident.ext == 'mzid': | |
41 #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name) | |
42 #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml': | |
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 | 83 --filter "mzRefiner $input_ident_name |
49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels | 84 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels |
50 thresholdScore=$data_processing.precursor_refinement.thresholdScore | 85 thresholdScore=$data_processing.precursor_refinement.thresholdScore |
51 thresholdValue=$data_processing.precursor_refinement.thresholdValue | 86 thresholdValue=$data_processing.precursor_refinement.thresholdValue |
52 thresholdStep=$data_processing.precursor_refinement.thresholdStep | 87 thresholdStep=$data_processing.precursor_refinement.thresholdStep |
53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps" | 88 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps assumeHighRes=1" |
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" | |
58 #end if | 89 #end if |
59 | 90 |
60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor" | 91 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor" |
61 --filter "chargeStatePredictor | 92 --filter "chargeStatePredictor |
62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge | 93 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge |
74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge | 105 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge |
75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge" | 106 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge" |
76 #end if | 107 #end if |
77 | 108 |
78 #for threshold_entry in $data_processing.thresholds | 109 #for threshold_entry in $data_processing.thresholds |
79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" | 110 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation" |
80 #end for | 111 #end for |
81 | 112 |
82 #if $data_processing.filter_mz_windows.do_mzwindow_filter | 113 #if $data_processing.filter_mz_windows.do_mzwindow_filter |
83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" | 114 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]" |
84 #end if | 115 #end if |
85 | 116 |
86 #if $data_processing.etd_filtering.do_etd_filtering | 117 #if $data_processing.etd_filtering.do_etd_filtering |
87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor | 118 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor |
88 $data_processing.etd_filtering.remove_charge_reduced | 119 $data_processing.etd_filtering.remove_charge_reduced |
89 $data_processing.etd_filtering.remove_neutral_loss | 120 $data_processing.etd_filtering.remove_neutral_loss |
90 $data_processing.etd_filtering.blanket_removal | 121 $data_processing.etd_filtering.blanket_removal |
91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units" | 122 $data_processing.etd_filtering.matching_tolerance$data_processing.etd_filtering.matching_tolerance_units" |
92 #end if | 123 #end if |
93 | 124 |
94 #if $data_processing.ms2denoise.denoise | 125 #if $data_processing.ms2denoise.denoise |
95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" | 126 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax" |
96 #end if | 127 #end if |
97 | 128 |
98 #if str($data_processing.ms2deisotope) == "true" | 129 #if str($data_processing.ms2deisotope) == "true" |
99 --filter "MS2Deisotope" | 130 --filter "MS2Deisotope" |
100 #end if | 131 #end if |
101 | 132 |
102 | 133 |
103 ## SCAN INCLUSION/EXCLUSION FILTERS | 134 ## SCAN INCLUSION/EXCLUSION FILTERS |
104 #if str($filtering.activation) != "false" | 135 #if str($filtering.activation) != "false" |
105 --filter "activation $filtering.activation" | 136 --filter "activation $filtering.activation" |
106 #end if | 137 #end if |
107 | 138 |
108 #if len($filtering.indices) > 0 | 139 #if len($filtering.indices) > 0 |
109 --filter "index | 140 --filter "index |
110 #for $index in $filtering.indices | 141 #for $index in $filtering.indices |
111 [${index.from},${index.to}] | 142 [${index.from},${index.to}] |
112 #end for | 143 #end for |
113 " | 144 " |
114 #end if | 145 #end if |
115 | 146 |
116 #if len($filtering.scan_numbers) > 0 | 147 #if len($filtering.scan_numbers) > 0 |
117 --filter "scanNumber | 148 --filter "scanNumber |
118 #for $scan_number in $filtering.scan_numbers | 149 #for $scan_number in $filtering.scan_numbers |
119 [${scan_number.from},${scan_number.to}] | 150 [${scan_number.from},${scan_number.to}] |
120 #end for | 151 #end for |
121 " | 152 " |
122 #end if | 153 #end if |
123 | 154 |
124 #if $filtering.strip_it.value | 155 #if $filtering.strip_it.value |
125 --filter "stripIT" | 156 --filter "stripIT" |
126 #end if | 157 #end if |
127 | 158 |
128 #if $filtering.filter_ms_levels.do_ms_level_filter | 159 #if $filtering.filter_ms_levels.do_ms_level_filter |
129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" | 160 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]" |
130 #end if | 161 #end if |
131 | 162 |
132 #if str($filtering.polarity) != "false" | 163 #if str($filtering.polarity) != "false" |
133 --filter "polarity $filtering.polarity" | 164 --filter "polarity $filtering.polarity" |
134 #end if | 165 #end if |
135 | 166 |
136 #if str($filtering.analyzer) != "false" | 167 #if str($filtering.analyzer) != "false" |
137 --filter "analyzer $filtering.analyzer" | 168 --filter "analyzer $filtering.analyzer" |
138 #end if | 169 #end if |
139 | 170 |
140 ## OUTPUT ENCODING | 171 ## OUTPUT ENCODING |
141 -- | |
142 #set $mz_encoding = str($settings.mz_encoding) | 172 #set $mz_encoding = str($settings.mz_encoding) |
143 #set $intensity_encoding = str($settings.intensity_encoding) | 173 #set $intensity_encoding = str($settings.intensity_encoding) |
144 #if $mz_encoding == $intensity_encoding | 174 #if $mz_encoding == $intensity_encoding |
145 #if $mz_encoding == "64" | 175 #if $mz_encoding == "64" |
146 --64 | 176 --64 |
152 --inten${intensity_encoding} | 182 --inten${intensity_encoding} |
153 #end if | 183 #end if |
154 | 184 |
155 #set binary_compression = str($settings.binary_compression) | 185 #set binary_compression = str($settings.binary_compression) |
156 #if $binary_compression == "zlib" | 186 #if $binary_compression == "zlib" |
157 --zlib | 187 --zlib |
158 #else if $binary_compression == "numpressLinearPic" | 188 #else if $binary_compression == "numpressLinearPic" |
159 --numpressLinear --numpressPic | 189 --numpressLinear --numpressPic |
160 #else if $binary_compression == "numpressLinearSlof" | 190 #else if $binary_compression == "numpressLinearSlof" |
161 --numpressLinear --numpressSlof | 191 --numpressLinear --numpressSlof |
162 #else if $binary_compression == "numpressLinear" | 192 #else if $binary_compression == "numpressLinear" |
163 --numpressLinear | 193 --numpressLinear |
164 #else if $binary_compression == "numpressPic" | 194 #else if $binary_compression == "numpressPic" |
165 --numpressPic | 195 --numpressPic |
166 #else if $binary_compression == "numpressSlof" | 196 #else if $binary_compression == "numpressSlof" |
167 --numpressSlof | 197 --numpressSlof |
168 #end if | 198 #end if |
169 | 199 |
170 #if $settings.gzip_compression | 200 #if $settings.gzip_compression |
171 --gzip | 201 --gzip |
172 #end if | 202 #end if |
173 | 203 |
204 #if $general_options.multi_run_output.do_multi_run_output == 'false': | |
205 --outfile '${os.path.splitext($basename)[0]}' | |
206 && sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' && sudo chown \$uid:\$gid '${output}' | |
207 #else | |
208 && sudo chown \$uid:\$gid 'outputs' -R | |
209 && ls -la outputs/ | |
210 #end if | |
211 | |
212 #if $data_processing.precursor_refinement.use_mzrefinement | |
213 && sudo mv '$output_refinement_name' '$output_refinement' && sudo chown \$uid:\$gid '$output_refinement' | |
214 #end if | |
174 ]]> | 215 ]]> |
175 </command> | 216 </command> |
176 </xml> | 217 </xml> |
177 | 218 |
178 <xml name="msconvertInputParameters"> | 219 <xml name="msconvertInputParameters"> |
220 <param name="license_agreement" type="boolean" label="Do you agree to the vendor licenses?" help="This tool uses proprietary vendor libraries; to run it you must agree to the vendor licenses. Read them at http://www.proteowizard.org/licenses.html"> | |
221 <validator type="expression" message="You must agree to the vendor licenses to run msconvert.">True == value</validator> | |
222 </param> | |
223 | |
179 <param name="output_type" type="select" label="Output Type"> | 224 <param name="output_type" type="select" label="Output Type"> |
180 <option value="mz5" selected="true">mz5</option> | 225 <option value="mz5" selected="true">mz5</option> |
181 <option value="mzML">mzML</option> | 226 <option value="mzML">mzML</option> |
182 <option value="mzXML">mzXML</option> | 227 <option value="mzXML">mzXML</option> |
183 <option value="mgf">mgf</option> | 228 <option value="mgf">mgf</option> |
184 <option value="ms2">ms2</option> | 229 <option value="ms2">ms2</option> |
185 </param> | 230 </param> |
186 | 231 |
187 <section name="data_processing" title="Data Processing Filters"> | 232 <section name="data_processing" title="Data Processing Filters"> |
188 | 233 <conditional name="peak_picking"> |
189 <conditional name="peak_picking"> | 234 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" /> |
190 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" /> | 235 <when value="false" /> |
191 <when value="false" /> | 236 <when value="true"> |
192 <when value="true"> | 237 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> |
193 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> | 238 <option value="1">MS1 Only (1)</option> |
194 <option value="1">MS1 Only (1)</option> | 239 <option value="2">MS2 Only (2)</option> |
195 <option value="2">MS2 Only (2)</option> | 240 <option value="2-">MS2 and on (2-)</option> |
196 <option value="2-">MS2 and on (2-)</option> | 241 <option value="1-" selected="true">All Levels (1-)</option> |
197 <option value="1-" selected="true">All Levels (1-)</option> | 242 </param> |
198 </param> | 243 <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)"> |
199 <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)"> | 244 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option> |
200 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option> | 245 <option value="cwt">CantWaiT - continuous wavelet transform</option> |
201 <option value="cwt">CantWaiT - continuous wavelet transform</option> | 246 </param> |
202 </param> | 247 </when> |
203 </when> | |
204 </conditional> | 248 </conditional> |
205 | 249 |
206 <conditional name="precursor_refinement"> | 250 <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" /> | 251 <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> | 252 <when value="false"></when> |
209 <when value="true"> | 253 <when value="true"> |
210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" /> | 254 <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+" /> | 255 <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." /> | 256 <sanitizer> |
257 <valid initial="string.letters" /> | |
258 </sanitizer> | |
259 </param> | |
260 <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."> | |
261 <sanitizer> | |
262 <valid initial="string.letters,string.digits"> | |
263 <add value="-" /> | |
264 </valid> | |
265 </sanitizer> | |
266 </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)." /> | 267 <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?" /> | 268 <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"> | 269 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels"> |
216 <option value="1">MS1 Only (1)</option> | 270 <option value="1">MS1 Only (1)</option> |
217 <option value="2">MS2 Only (2)</option> | 271 <option value="2">MS2 Only (2)</option> |
367 <option value="IT">Ion trap</option> | 421 <option value="IT">Ion trap</option> |
368 <option value="TOF">Time of flight</option> | 422 <option value="TOF">Time of flight</option> |
369 </param> | 423 </param> |
370 </section> | 424 </section> |
371 | 425 |
426 <section name="general_options" title="General Options"> | |
427 <param argument="--combineIonMobilitySpectra" type="boolean" label="Combine ion mobility spectra" help="When false, each mobility scan is written as a separate spectrum. When true, each retention time point will have a single merged scan. For Bruker TIMS spectra, the ion mobilities will be preserved in a separate binaryDataArray, and for TIMS PASEF MS2s, each precursor will be merged separately." /> | |
428 | |
429 <conditional name="scan_summing"> | |
430 <param name="do_scan_summing" type="boolean" truevalue="true" falsevalue="false" label="Sum adjacent scans" help="Sums MS2 sub-scans whose precursors are similar in the m/z, scan time, and/or ion mobility dimensions. It is useful for some Waters DDA data and Bruker PASEF data, where sub-scans should be summed together to increase the SNR" /> | |
431 <when value="false" /> | |
432 <when value="true"> | |
433 <param name="precursorTol" type="float" label="Precursor m/z tolerance" value="0.05" min="0" optional="true" help="Spectra with precursor m/z values with a difference less than this tolerance are summed together." /> | |
434 <param name="scanTimeTol" type="float" label="Scan time tolerance" value="10.0" min="0" optional="true" help="Spectra with scan times with a difference less than this tolerance (in seconds) are summed together." /> | |
435 <param name="ionMobilityTol" type="float" label="Ion mobility tolerance" value="0.01" min="0" optional="true" help="Spectra with ion mobility values with a difference less than this tolerance are summed together. Only relevant for ion mobility spectra." /> | |
436 </when> | |
437 </conditional> | |
438 | |
439 <param argument="--simAsSpectra" type="boolean" label="SIM as Spectra" help="Write selected ion monitoring as spectra, not chromatograms" /> | |
440 <param argument="--srmAsSpectra" type="boolean" label="SRM as Spectra" help="Write selected reaction monitoring as spectra, not chromatograms" /> | |
441 <param argument="--acceptZeroLengthSpectra" type="boolean" label="Accept zero-length spectra" help="Some vendor readers have an efficient way of filtering out empty spectra, but it takes more time to open the file" /> | |
442 <param argument="--ignoreUnknownInstrumentError" type="boolean" label="Ignore unknown instrument error" help="If true, if an instrument cannot be determined from a vendor file, it will not be an error" /> | |
443 | |
444 <conditional name="multi_run_output"> | |
445 <param name="do_multi_run_output" type="boolean" truevalue="true" falsevalue="false" label="Output multiple runs per file" help="Some input types can store multiple runs (samples) in a single file (e.g. WIFF). Each run must be written to a separate output file, so check this option if you want to output all runs for a file (each file will create a dataset collection)" /> | |
446 <when value="false"> | |
447 <param argument="--runIndexSet" type="integer" label="Select a single run for multi-run sources" value="0" min="0" help="For multi-run sources (e.g. WIFF), select only the specified run index (first run is index 0)" /> | |
448 </when> | |
449 <when value="true"> | |
450 <repeat name="run_index_set" title="Select runs for multi-run sources" help="For multi-run sources (e.g. WIFF), select only the specified run indices"> | |
451 <param name="from" type="integer" label="Run Index From" value="0" min="0" optional="false" /> | |
452 <param name="to" type="integer" label="Run Index To" value="0" min="0" optional="true" /> | |
453 </repeat> | |
454 </when> | |
455 </conditional> | |
456 </section> | |
372 | 457 |
373 <section name="settings" title="Output Encoding Settings"> | 458 <section name="settings" title="Output Encoding Settings"> |
374 <param type="select" name="mz_encoding" label="m/z Encoding Precision"> | 459 <param type="select" name="mz_encoding" label="m/z Encoding Precision"> |
375 <option value="64" selected="true">64</option> | 460 <option value="64" selected="true">64</option> |
376 <option value="32">32</option> | 461 <option value="32">32</option> |
392 </section> | 477 </section> |
393 </xml> | 478 </xml> |
394 | 479 |
395 <xml name="msconvertOutput"> | 480 <xml name="msconvertOutput"> |
396 <outputs> | 481 <outputs> |
397 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" > | 482 <data format="mzml" name="output" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}" > |
483 <filter>general_options['multi_run_output']['do_multi_run_output'] == False</filter> | |
398 <change_format> | 484 <change_format> |
399 <when input="output_type" value="mz5" format="mz5" /> | 485 <when input="output_type" value="mz5" format="mz5" /> |
400 <when input="output_type" value="mzXML" format="mzxml" /> | 486 <when input="output_type" value="mzXML" format="mzxml" /> |
401 <when input="output_type" value="ms2" format="ms2" /> | 487 <when input="output_type" value="ms2" format="ms2" /> |
402 <when input="output_type" value="mgf" format="mgf" /> | 488 <when input="output_type" value="mgf" format="mgf" /> |
403 </change_format> | 489 </change_format> |
404 </data> | 490 </data> |
405 <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv"> | 491 <data format="tsv" name="output_refinement" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.mzRefinement.tsv"> |
406 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> | 492 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter> |
407 </data> | 493 </data> |
494 <collection name="multi_run_output_list" type="list" label="${($input.name[:-4] if $input.name.endswith('.tar') else $input.name).rsplit('.',1)[0]}.${output_type}"> | |
495 <filter>general_options['multi_run_output']['do_multi_run_output'] == True</filter> | |
496 <discover_datasets pattern="__name_and_ext__" directory="outputs" /> | |
497 </collection> | |
408 </outputs> | 498 </outputs> |
409 </xml> | 499 </xml> |
410 | 500 |
411 | 501 |
412 <xml name="msconvert_tests"> | 502 <xml name="msconvert_tests"> |
413 <test> | 503 <test> |
414 <param name="input" value="small.mzML" /> | 504 <param name="input" value="small.mzML" /> |
505 <param name="license_agreement" value="true" /> | |
415 <param name="output_type" value="mzML" /> | 506 <param name="output_type" value="mzML" /> |
416 <param name="pick_peaks" value="true" /> | 507 <param name="pick_peaks" value="true" /> |
417 <param name="pick_peaks_algorithm" value="cwt" /> | 508 <param name="pick_peaks_algorithm" value="cwt" /> |
418 <param name="pick_peaks_ms_levels" value="1-" /> | 509 <param name="pick_peaks_ms_levels" value="1-" /> |
419 <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> | 510 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> |
511 </test> | |
512 <test> | |
513 <param name="input" value="small.RAW" ftype="thermo.raw" /> | |
514 <param name="license_agreement" value="true" /> | |
515 <param name="output_type" value="mzML" /> | |
516 <param name="pick_peaks" value="true" /> | |
517 <param name="pick_peaks_algorithm" value="vendor" /> | |
518 <param name="pick_peaks_ms_levels" value="1-" /> | |
519 <output name="output" file="small-peakpicking-vendor-allMS.mzML" lines_diff="4" /> | |
520 </test> | |
521 <test> | |
522 <param name="input" value="ThyroglobMRM000003.d.tar" /> | |
523 <param name="license_agreement" value="true" /> | |
524 <param name="output_type" value="mzML" /> | |
525 <param name="combineIonMobilitySpectra" value="true" /> | |
526 <param name="do_scan_summing" value="true" /> | |
527 <output name="output" file="ThyroglobMRM000003.mzML" lines_diff="4" /> | |
528 </test> | |
529 <test> | |
530 <param name="input" value="MassLynxTest.raw.tar" /> | |
531 <param name="license_agreement" value="true" /> | |
532 <param name="output_type" value="mzML" /> | |
533 <output name="output" file="MassLynxTest.mzML" lines_diff="4" /> | |
534 </test> | |
535 <test> | |
536 <param name="input" value="AgilentMassHunterTest.d.tar" /> | |
537 <param name="license_agreement" value="true" /> | |
538 <param name="output_type" value="mzXML" /> | |
539 <output name="output" file="AgilentMassHunterTest.mzXML" lines_diff="4" /> | |
540 </test> | |
541 <test> | |
542 <param name="input" value="BrukerBafTest.d.tar" /> | |
543 <param name="license_agreement" value="true" /> | |
544 <param name="output_type" value="mzML" /> | |
545 <param name="pick_peaks" value="true" /> | |
546 <param name="pick_peaks_algorithm" value="vendor" /> | |
547 <param name="pick_peaks_ms_levels" value="1-" /> | |
548 <output name="output" file="BrukerBafTest.mzML" lines_diff="4" /> | |
549 </test> | |
550 <test> | |
551 <param name="input" value="SciexTest.wiff.tar" /> | |
552 <param name="license_agreement" value="true" /> | |
553 <param name="output_type" value="mzML" /> | |
554 <param name="do_multi_run_output" value="false" /> | |
555 <param name="runIndexSet" value="0" /> | |
556 <output name="output" file="SciexTest-HPINalone.mzML" lines_diff="4" /> | |
557 </test> | |
558 <test> | |
559 <param name="input" value="SciexTest.wiff.tar" /> | |
560 <param name="license_agreement" value="true" /> | |
561 <param name="output_type" value="mzXML" /> | |
562 <param name="do_multi_run_output" value="false" /> | |
563 <param name="runIndexSet" value="0" /> | |
564 <param name="indices_0|from" value="0" /> | |
565 <param name="indices_0|to" value="499" /> | |
566 <param name="srmAsSpectra" value="true" /> | |
567 <output name="output" file="SciexTest-HPINalone-srmAsSpectra.mzXML" lines_diff="4" /> | |
568 </test> | |
569 <test> | |
570 <param name="input" value="SciexTest.wiff.tar" /> | |
571 <param name="license_agreement" value="true" /> | |
572 <param name="output_type" value="mzXML" /> | |
573 <param name="do_multi_run_output" value="false" /> | |
574 <param name="runIndexSet" value="1" /> | |
575 <param name="indices_0|from" value="0" /> | |
576 <param name="indices_0|to" value="499" /> | |
577 <param name="srmAsSpectra" value="true" /> | |
578 <output name="output" file="SciexTest-HPINalone-NE-srmAsSpectra.mzXML" lines_diff="4" /> | |
579 </test> | |
580 <test> | |
581 <param name="input" value="SciexTest.wiff.tar" /> | |
582 <param name="license_agreement" value="true" /> | |
583 <param name="output_type" value="mzML" /> | |
584 <param name="do_multi_run_output" value="true" /> | |
585 <param name="run_index_set_0|from" value="0" /> | |
586 <param name="run_index_set_0|to" value="1" /> | |
587 <output_collection name="multi_run_output_list" type="list"> | |
588 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> | |
589 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> | |
590 </output_collection> | |
591 </test> | |
592 <test> | |
593 <param name="input" value="SciexTest.wiff.tar" /> | |
594 <param name="license_agreement" value="true" /> | |
595 <param name="output_type" value="mzML" /> | |
596 <param name="do_multi_run_output" value="true" /> | |
597 <output_collection name="multi_run_output_list" type="list"> | |
598 <element name="SciexTest-HPINalone" file="SciexTest-HPINalone.mzML" lines_diff="4" /> | |
599 <element name="SciexTest-HPINalone+NE" file="SciexTest-HPINalone-NE.mzML" lines_diff="4" /> | |
600 </output_collection> | |
420 </test> | 601 </test> |
421 | 602 |
422 <!-- this data file only has profile MS1, so the result is the same --> | 603 <!-- this data file only has profile MS1, so the result is the same --> |
423 <test> | 604 <test> |
424 <param name="input" value="small.mzML" /> | 605 <param name="input" value="small.mzML" /> |
606 <param name="license_agreement" value="true" /> | |
425 <param name="output_type" value="mzML" /> | 607 <param name="output_type" value="mzML" /> |
426 <param name="pick_peaks" value="true" /> | 608 <param name="pick_peaks" value="true" /> |
427 <param name="pick_peaks_algorithm" value="cwt" /> | 609 <param name="pick_peaks_algorithm" value="cwt" /> |
428 <param name="pick_peaks_ms_levels" value="1" /> | 610 <param name="pick_peaks_ms_levels" value="1" /> |
429 <output name="output" file="small-peakpicking-cwt-allMS.mzML" /> | 611 <output name="output" file="small-peakpicking-cwt-allMS.mzML" lines_diff="8" /> |
430 </test> | 612 </test> |
431 <test> | 613 <test> |
432 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 614 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
615 <param name="license_agreement" value="true" /> | |
433 <param name="output_type" value="mz5" /> | 616 <param name="output_type" value="mz5" /> |
434 <param name="mz_encoding" value="64" /> | 617 <param name="mz_encoding" value="64" /> |
435 <param name="intensity_encoding" value="64" /> | 618 <param name="intensity_encoding" value="64" /> |
436 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" /> | 619 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="150000" /> |
437 </test> | 620 </test> |
438 <test> | 621 <test> |
439 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 622 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
623 <param name="license_agreement" value="true" /> | |
440 <param name="output_type" value="mzXML" /> | 624 <param name="output_type" value="mzXML" /> |
441 <param name="mz_encoding" value="32" /> | 625 <param name="mz_encoding" value="32" /> |
442 <param name="intensity_encoding" value="32" /> | 626 <param name="intensity_encoding" value="32" /> |
443 <output name="output" file="small-zlib-32.mzXML" /> | 627 <output name="output" file="small-zlib-32.mzXML" lines_diff="6" /> |
444 </test> | 628 </test> |
445 <!-- TODO: how to test gzipped output? | 629 <!-- TODO: how to test gzipped output? |
446 <test> | 630 <test> |
447 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 631 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
448 <param name="output_type" value="mzXML" /> | 632 <param name="output_type" value="mzXML" /> |
462 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> | 646 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" /> |
463 </test>--> | 647 </test>--> |
464 | 648 |
465 <test> | 649 <test> |
466 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 650 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
467 <param name="output_type" value="mzML" /> | 651 <param name="license_agreement" value="true" /> |
468 <param name="binary_compression" value="numpressLinearPic" /> | 652 <param name="output_type" value="mzML" /> |
469 <output name="output" file="small-numpressLP.mzML" /> | 653 <param name="binary_compression" value="numpressLinearPic" /> |
470 </test> | 654 <output name="output" file="small-numpressLP.mzML" lines_diff="114" /> |
471 | 655 </test> |
472 <test> | 656 |
473 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 657 <test> |
658 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | |
659 <param name="license_agreement" value="true" /> | |
474 <param name="output_type" value="mzML" /> | 660 <param name="output_type" value="mzML" /> |
475 <param name="binary_compression" value="numpressLinearSlof" /> | 661 <param name="binary_compression" value="numpressLinearSlof" /> |
476 <output name="output" file="small-numpressLS.mzML" /> | 662 <output name="output" file="small-numpressLS.mzML" lines_diff="114" /> |
477 </test> | 663 </test> |
478 | 664 |
479 <test> | 665 <test> |
480 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 666 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
667 <param name="license_agreement" value="true" /> | |
481 <param name="output_type" value="mzML" /> | 668 <param name="output_type" value="mzML" /> |
482 <param name="binary_compression" value="numpressLinear" /> | 669 <param name="binary_compression" value="numpressLinear" /> |
483 <output name="output" file="small-numpressL.mzML" /> | 670 <output name="output" file="small-numpressL.mzML" lines_diff="114" /> |
484 </test> | 671 </test> |
485 | 672 |
486 <test> | 673 <test> |
487 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 674 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
675 <param name="license_agreement" value="true" /> | |
488 <param name="output_type" value="mzML" /> | 676 <param name="output_type" value="mzML" /> |
489 <param name="binary_compression" value="numpressPic" /> | 677 <param name="binary_compression" value="numpressPic" /> |
490 <output name="output" file="small-numpressP.mzML" /> | 678 <output name="output" file="small-numpressP.mzML" lines_diff="114" /> |
491 </test> | 679 </test> |
492 | 680 |
493 <test> | 681 <test> |
494 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 682 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
683 <param name="license_agreement" value="true" /> | |
495 <param name="output_type" value="mzML" /> | 684 <param name="output_type" value="mzML" /> |
496 <param name="binary_compression" value="numpressSlof" /> | 685 <param name="binary_compression" value="numpressSlof" /> |
497 <output name="output" file="small-numpressS.mzML" /> | 686 <output name="output" file="small-numpressS.mzML" lines_diff="114" /> |
498 </test> | 687 </test> |
499 | 688 |
500 <test> | 689 <test> |
501 <param name="input" value="Rpal_01.mz5" /> | 690 <param name="input" value="Rpal_01.mz5" /> |
691 <param name="license_agreement" value="true" /> | |
502 <param name="output_type" value="mzML" /> | 692 <param name="output_type" value="mzML" /> |
503 <param name="binary_compression" value="numpressLinearPic" /> | 693 <param name="binary_compression" value="numpressLinearPic" /> |
504 <param name="use_mzrefinement" value="true" /> | 694 <param name="use_mzrefinement" value="true" /> |
505 <param name="input_ident" value="Rpal_01.pepXML.gz" /> | 695 <param name="input_ident" value="Rpal_01.pepXML" /> |
506 <param name="thresholdScore" value="mvh" /> | 696 <param name="thresholdScore" value="mvh" /> |
507 <param name="thresholdValue" value="40-" /> | 697 <param name="thresholdValue" value="40-" /> |
508 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> | 698 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" /> |
509 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> | 699 <output name="output_refinement" file="Rpal_01.pepXML.mzRefinement.tsv" /> |
510 </test> | 700 </test> |
511 | 701 |
512 <test> | 702 <test> |
513 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 703 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
704 <param name="license_agreement" value="true" /> | |
514 <param name="output_type" value="mzML" /> | 705 <param name="output_type" value="mzML" /> |
515 <param name="binary_compression" value="numpressLinearPic" /> | 706 <param name="binary_compression" value="numpressLinearPic" /> |
516 <param name="charge_state_calculation_method" value="predictor" /> | 707 <param name="charge_state_calculation_method" value="predictor" /> |
517 <param name="predictor_overrideExistingCharge" value="true" /> | 708 <param name="predictor_overrideExistingCharge" value="true" /> |
518 <param name="minMultipleCharge" value="2" /> | 709 <param name="minMultipleCharge" value="2" /> |
519 <param name="maxMultipleCharge" value="5" /> | 710 <param name="maxMultipleCharge" value="5" /> |
520 <param name="singleChargeFractionTIC" value="0.95" /> | 711 <param name="singleChargeFractionTIC" value="0.95" /> |
521 <param name="maxKnownCharge" value="8" /> | 712 <param name="maxKnownCharge" value="8" /> |
522 <output name="output" file="small-chargeStatePredictor.mzML" /> | 713 <output name="output" file="small-chargeStatePredictor.mzML" lines_diff="114" /> |
523 </test> | 714 </test> |
524 <test> | 715 <test> |
525 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 716 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
717 <param name="license_agreement" value="true" /> | |
526 <param name="output_type" value="mzML" /> | 718 <param name="output_type" value="mzML" /> |
527 <param name="binary_compression" value="numpressLinearPic" /> | 719 <param name="binary_compression" value="numpressLinearPic" /> |
528 <param name="charge_state_calculation_method" value="turbocharger" /> | 720 <param name="charge_state_calculation_method" value="turbocharger" /> |
529 <param name="minCharge" value="1" /> | 721 <param name="minCharge" value="1" /> |
530 <param name="maxCharge" value="5" /> | 722 <param name="maxCharge" value="5" /> |
531 <param name="precursorsBefore" value="1" /> | 723 <param name="precursorsBefore" value="1" /> |
532 <param name="precursorsAfter" value="1" /> | 724 <param name="precursorsAfter" value="1" /> |
533 <param name="halfIsoWidth" value="1.5" /> | 725 <param name="halfIsoWidth" value="1.5" /> |
534 <param name="defaultMinCharge" value="1" /> | 726 <param name="defaultMinCharge" value="1" /> |
535 <param name="defaultMaxCharge" value="5" /> | 727 <param name="defaultMaxCharge" value="5" /> |
536 <output name="output" file="small-turbocharger.mzML" /> | 728 <output name="output" file="small-turbocharger.mzML" lines_diff="114" /> |
537 </test> | 729 </test> |
538 <test> | 730 <test> |
539 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" /> | 731 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" /> |
732 <param name="license_agreement" value="true" /> | |
540 <param name="output_type" value="mzML" /> | 733 <param name="output_type" value="mzML" /> |
541 <param name="do_etd_filtering" value="true" /> | 734 <param name="do_etd_filtering" value="true" /> |
542 <param name="remove_precursor" value="true" /> | 735 <param name="remove_precursor" value="true" /> |
543 <param name="remove_charge_reduced" value="true" /> | 736 <param name="remove_charge_reduced" value="true" /> |
544 <param name="remove_neutral_loss" value="false" /> | 737 <param name="remove_neutral_loss" value="false" /> |
548 <param name="binary_compression" value="numpressLinearPic" /> | 741 <param name="binary_compression" value="numpressLinearPic" /> |
549 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" /> | 742 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" /> |
550 </test> | 743 </test> |
551 <test> | 744 <test> |
552 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 745 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
746 <param name="license_agreement" value="true" /> | |
553 <param name="output_type" value="mzML" /> | 747 <param name="output_type" value="mzML" /> |
554 <param name="thresholds_0|threshold_type" value="count" /> | 748 <param name="thresholds_0|threshold_type" value="count" /> |
555 <param name="thresholds_0|value" value="100" /> | 749 <param name="thresholds_0|value" value="100" /> |
556 <param name="thresholds_0|orientation" value="most-intense" /> | 750 <param name="thresholds_0|orientation" value="most-intense" /> |
557 <param name="thresholds_1|threshold_type" value="absolute" /> | 751 <param name="thresholds_1|threshold_type" value="absolute" /> |
558 <param name="thresholds_1|value" value="1" /> | 752 <param name="thresholds_1|value" value="1" /> |
559 <param name="thresholds_1|orientation" value="most-intense" /> | 753 <param name="thresholds_1|orientation" value="most-intense" /> |
560 <param name="binary_compression" value="numpressLinearPic" /> | 754 <param name="binary_compression" value="numpressLinearPic" /> |
561 <output name="output" file="small-threshold.mzML" /> | 755 <output name="output" file="small-threshold.mzML" lines_diff="114" /> |
562 </test> | 756 </test> |
563 <test> | 757 <test> |
564 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 758 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
759 <param name="license_agreement" value="true" /> | |
565 <param name="output_type" value="mzML" /> | 760 <param name="output_type" value="mzML" /> |
566 <param name="do_mzwindow_filter" value="true" /> | 761 <param name="do_mzwindow_filter" value="true" /> |
567 <param name="mz_window_from" value="420" /> | 762 <param name="mz_window_from" value="420" /> |
568 <param name="mz_window_to" value="840" /> | 763 <param name="mz_window_to" value="840" /> |
569 <param name="binary_compression" value="numpressLinearPic" /> | 764 <param name="binary_compression" value="numpressLinearPic" /> |
570 <output name="output" file="small-mzWindow.mzML" /> | 765 <output name="output" file="small-mzWindow.mzML" lines_diff="114" /> |
571 </test> | 766 </test> |
572 <test> | 767 <test> |
573 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 768 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
769 <param name="license_agreement" value="true" /> | |
574 <param name="output_type" value="mzML" /> | 770 <param name="output_type" value="mzML" /> |
575 <param name="denoise" value="true" /> | 771 <param name="denoise" value="true" /> |
576 <param name="num_peaks" value="10" /> | 772 <param name="num_peaks" value="10" /> |
577 <param name="window_width" value="40" /> | 773 <param name="window_width" value="40" /> |
578 <param name="relax" value="false" /> | 774 <param name="relax" value="false" /> |
579 <param name="binary_compression" value="numpressLinearPic" /> | 775 <param name="binary_compression" value="numpressLinearPic" /> |
580 <output name="output" file="small-denoise.mzML" /> | 776 <output name="output" file="small-denoise.mzML" lines_diff="114" /> |
581 </test> | 777 </test> |
582 <test> | 778 <test> |
583 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 779 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
780 <param name="license_agreement" value="true" /> | |
584 <param name="output_type" value="mzML" /> | 781 <param name="output_type" value="mzML" /> |
585 <param name="ms2deisotope" value="true" /> | 782 <param name="ms2deisotope" value="true" /> |
586 <param name="binary_compression" value="numpressLinearPic" /> | 783 <param name="binary_compression" value="numpressLinearPic" /> |
587 <output name="output" file="small-deisotope.mzML" /> | 784 <output name="output" file="small-deisotope.mzML" lines_diff="114" /> |
588 </test> | 785 </test> |
589 <test> | 786 <test> |
590 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 787 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
788 <param name="license_agreement" value="true" /> | |
591 <param name="output_type" value="mzML" /> | 789 <param name="output_type" value="mzML" /> |
592 <param name="activation" value="CID" /> | 790 <param name="activation" value="CID" /> |
593 <param name="binary_compression" value="numpressLinearPic" /> | 791 <param name="binary_compression" value="numpressLinearPic" /> |
594 <output name="output" file="small-activation.mzML" /> | 792 <output name="output" file="small-activation.mzML" lines_diff="114" /> |
595 </test> | 793 </test> |
596 <test> | 794 <test> |
597 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 795 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
796 <param name="license_agreement" value="true" /> | |
598 <param name="output_type" value="mzML" /> | 797 <param name="output_type" value="mzML" /> |
599 <param name="indices_0|from" value="2" /> | 798 <param name="indices_0|from" value="2" /> |
600 <param name="indices_0|to" value="4" /> | 799 <param name="indices_0|to" value="4" /> |
601 <param name="indices_1|from" value="10" /> | 800 <param name="indices_1|from" value="10" /> |
602 <param name="indices_1|to" value="10" /> | 801 <param name="indices_1|to" value="10" /> |
603 <param name="indices_2|from" value="13" /> | 802 <param name="indices_2|from" value="13" /> |
604 <param name="indices_2|to" value="15" /> | 803 <param name="indices_2|to" value="15" /> |
605 <param name="binary_compression" value="numpressLinearPic" /> | 804 <param name="binary_compression" value="numpressLinearPic" /> |
606 <output name="output" file="small-index-filter.mzML" /> | 805 <output name="output" file="small-index-filter.mzML" lines_diff="32" /> |
607 </test> | 806 </test> |
608 <test> | 807 <test> |
609 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 808 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
809 <param name="license_agreement" value="true" /> | |
610 <param name="output_type" value="mzML" /> | 810 <param name="output_type" value="mzML" /> |
611 <param name="strip_it" value="true" /> | 811 <param name="strip_it" value="true" /> |
612 <param name="binary_compression" value="numpressLinearPic" /> | 812 <param name="binary_compression" value="numpressLinearPic" /> |
613 <output name="output" file="small-strip-it.mzML" /> | 813 <output name="output" file="small-strip-it.mzML" lines_diff="100" /> |
614 </test> | 814 </test> |
615 <test> | 815 <test> |
616 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 816 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
817 <param name="license_agreement" value="true" /> | |
617 <param name="output_type" value="mzML" /> | 818 <param name="output_type" value="mzML" /> |
618 <param name="do_ms_level_filter" value="true" /> | 819 <param name="do_ms_level_filter" value="true" /> |
619 <param name="ms_level_from" value="2" /> | 820 <param name="ms_level_from" value="2" /> |
620 <param name="ms_level_to" value="2" /> | 821 <param name="ms_level_to" value="2" /> |
621 <param name="binary_compression" value="numpressLinearPic" /> | 822 <param name="binary_compression" value="numpressLinearPic" /> |
622 <output name="output" file="small-ms-level-filter.mzML" /> | 823 <output name="output" file="small-ms-level-filter.mzML" lines_diff="86" /> |
623 </test> | 824 </test> |
624 <test> | 825 <test> |
625 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 826 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
827 <param name="license_agreement" value="true" /> | |
626 <param name="output_type" value="mzML" /> | 828 <param name="output_type" value="mzML" /> |
627 <param name="polarity" value="positive" /> | 829 <param name="polarity" value="positive" /> |
628 <param name="binary_compression" value="numpressLinearPic" /> | 830 <param name="binary_compression" value="numpressLinearPic" /> |
629 <output name="output" file="small-polarity-filter.mzML" /> | 831 <output name="output" file="small-polarity-filter.mzML" lines_diff="114" /> |
630 </test> | 832 </test> |
631 <test> | 833 <test> |
632 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 834 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
835 <param name="license_agreement" value="true" /> | |
633 <param name="output_type" value="mzML" /> | 836 <param name="output_type" value="mzML" /> |
634 <param name="analyzer" value="IT" /> | 837 <param name="analyzer" value="IT" /> |
635 <param name="binary_compression" value="numpressLinearPic" /> | 838 <param name="binary_compression" value="numpressLinearPic" /> |
636 <output name="output" file="small-analyzer-filter.mzML" /> | 839 <output name="output" file="small-analyzer-filter.mzML" lines_diff="100" /> |
637 </test> | 840 </test> |
638 <test> | 841 <test> |
639 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> | 842 <param name="input" value="small-peakpicking-cwt-allMS.mzML" /> |
843 <param name="license_agreement" value="true" /> | |
640 <param name="output_type" value="mzML" /> | 844 <param name="output_type" value="mzML" /> |
641 <param name="scan_numbers_0|from" value="3" /> | 845 <param name="scan_numbers_0|from" value="3" /> |
642 <param name="scan_numbers_0|to" value="5" /> | 846 <param name="scan_numbers_0|to" value="5" /> |
643 <param name="scan_numbers_1|from" value="11" /> | 847 <param name="scan_numbers_1|from" value="11" /> |
644 <param name="scan_numbers_1|to" value="11" /> | 848 <param name="scan_numbers_1|to" value="11" /> |
645 <param name="scan_numbers_2|from" value="14" /> | 849 <param name="scan_numbers_2|from" value="14" /> |
646 <param name="scan_numbers_2|to" value="16" /> | 850 <param name="scan_numbers_2|to" value="16" /> |
647 <param name="binary_compression" value="numpressLinearPic" /> | 851 <param name="binary_compression" value="numpressLinearPic" /> |
648 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above --> | 852 <output name="output" file="small-index-filter.mzML" lines_diff="86"/> <!-- the scan numbers here produce the same output as the index test above --> |
649 </test> | 853 </test> |
650 <!--<test> | 854 <!--<test> |
651 <param name="input" value="small.mzML" /> | 855 <param name="input" value="small.mzML" /> |
652 <param name="output_type" value="mzML" /> | 856 <param name="output_type" value="mzML" /> |
653 <param name="binary_compression" value="numpressLinearPic" /> | 857 <param name="binary_compression" value="numpressLinearPic" /> |
655 </test>--> | 859 </test>--> |
656 </xml> | 860 </xml> |
657 <xml name="msconvert_help"> | 861 <xml name="msconvert_help"> |
658 **What it does** | 862 **What it does** |
659 | 863 |
660 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. | 864 Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available. |
661 | 865 |
662 You can view the original documentation here_. | 866 You can view the original documentation here_. |
663 | 867 |
664 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html | 868 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html |
665 </xml> | 869 </xml> |