Mercurial > repos > galaxyp > msconvert_nix
comparison msconvert_macros.xml @ 1:7016f1f10f42 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit d56659dd48f8c554a832787e71aca6ae65c90848
author | galaxyp |
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date | Tue, 14 Mar 2017 16:45:30 -0400 |
parents | baa6c072fccc |
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0:baa6c072fccc | 1:7016f1f10f42 |
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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" /> |