annotate msconvert_macros.xml @ 9:dd4ba10d0c45 draft

planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 16:43:07 -0500
parents
children 9d5de24e6ef7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
1 <macros>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
2 <xml name="generic_requirements">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
3 <requirements>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
4 <requirement type="package" version="3.0.9016">proteowizard</requirement>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
5 </requirements>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
6 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
7 <token name="@VERSION@">3.0</token>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
8
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
9 <xml name="msconvertCommand">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
10 <command interpreter="python">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
11 <![CDATA[
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
12 #import re
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
13 #set $ext = $input.ext
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
14 msconvert_wrapper.py
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
15 #if $ext == 'wiff':
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
16 #set basename = 'absciex'
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
17 #if hasattr($input, 'display_name')
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
18 #set basename = $re.sub('\W','_',$input.display_name)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
19 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
20 --input=${input.extra_files_path}/wiff
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
21 --input_name='${basename}.wiff
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
22 --implicit=${input.extra_files_path}/wiff_scan
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
23 --input=${input.extra_files_path}/wiff_scan
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
24 --input_name='${basename}.wiff.scan
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
25 #else
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
26 --input=${input}
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
27 #if hasattr($input, 'display_name')
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
28 --input_name='${input.display_name}'
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
29 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
30 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
31 --output=${output}
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
32 ## BEGIN_VERSION_DEFAULT
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
33 --fromextension=$ext
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
34 ## END_VERSION_DEFAULT
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
35 --toextension=${output_type}
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
36
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
37 ## DATA PROCESSING FILTERS (NOTE: FOR VENDOR METHOD TO WORK, PEAK PICKING MUST BE THE FIRST FILTER!)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
38 #if $data_processing.precursor_refinement.use_mzrefinement
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
39 #set $input_ident_name = $re.sub('\W','_',$data_processing.precursor_refinement.input_ident.display_name)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
40 #if $data_processing.precursor_refinement.input_ident.ext == 'mzid':
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
41 #set $input_ident_name = $re.sub('(?i)([.]?mzid)*$','.mzid',$input_ident_name)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
42 #elif $data_processing.precursor_refinement.input_ident.ext == 'pepxml':
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
43 #set $input_ident_name = $re.sub('(?i)([.]?pep[.]?xml)*$','.pep.xml',$input_ident_name)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
44 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
45 --ident=$data_processing.precursor_refinement.input_ident
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
46 --ident_name=$input_ident_name
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
47 --refinement=$output_refinement
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
48 --filter "mzRefiner $input_ident_name
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
49 msLevels=$data_processing.precursor_refinement.precursor_refinement_ms_levels
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
50 thresholdScore=$data_processing.precursor_refinement.thresholdScore
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
51 thresholdValue=$data_processing.precursor_refinement.thresholdValue
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
52 thresholdStep=$data_processing.precursor_refinement.thresholdStep
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
53 maxSteps=$data_processing.precursor_refinement.thresholdMaxSteps"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
54 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
55
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
56 #if $data_processing.peak_picking.pick_peaks
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
57 --filter "peakPicking $data_processing.peak_picking.pick_peaks_algorithm msLevel=$data_processing.peak_picking.pick_peaks_ms_levels"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
58 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
59
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
60 #if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "predictor"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
61 --filter "chargeStatePredictor
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
62 overrideExistingCharge=$data_processing.charge_state_calculation.predictor_overrideExistingCharge
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
63 minMultipleCharge=$data_processing.charge_state_calculation.minMultipleCharge
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
64 maxMultipleCharge=$data_processing.charge_state_calculation.maxMultipleCharge
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
65 singleChargeFractionTIC=$data_processing.charge_state_calculation.singleChargeFractionTIC
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
66 maxKnownCharge=$data_processing.charge_state_calculation.maxKnownCharge"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
67 #else if str($data_processing.charge_state_calculation.charge_state_calculation_method) == "turbocharger"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
68 --filter "turbocharger
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
69 minCharge=$data_processing.charge_state_calculation.minCharge
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
70 maxCharge=$data_processing.charge_state_calculation.maxCharge
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
71 precursorsBefore=$data_processing.charge_state_calculation.precursorsBefore
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
72 precursorsAfter=$data_processing.charge_state_calculation.precursorsAfter
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
73 halfIsoWidth=$data_processing.charge_state_calculation.halfIsoWidth
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
74 defaultMinCharge=$data_processing.charge_state_calculation.defaultMinCharge
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
75 defaultMaxCharge=$data_processing.charge_state_calculation.defaultMaxCharge"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
76 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
77
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
78 #for threshold_entry in $data_processing.thresholds
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
79 --filter "threshold $threshold_entry.threshold_type $threshold_entry.value $threshold_entry.orientation"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
80 #end for
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
81
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
82 #if $data_processing.filter_mz_windows.do_mzwindow_filter
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
83 --filter "mzWindow [$data_processing.filter_mz_windows.mz_window_from,$data_processing.filter_mz_windows.mz_window_to]"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
84 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
85
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
86 #if $data_processing.etd_filtering.do_etd_filtering
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
87 --filter "ETDFilter $data_processing.etd_filtering.remove_precursor
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
88 $data_processing.etd_filtering.remove_charge_reduced
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
89 $data_processing.etd_filtering.remove_neutral_loss
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
90 $data_processing.etd_filtering.blanket_removal
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
91 $data_processing.etd_filtering.matching_tolerance $data_processing.etd_filtering.matching_tolerance_units"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
92 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
93
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
94 #if $data_processing.ms2denoise.denoise
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
95 --filter "MS2Denoise $data_processing.ms2denoise.num_peaks $data_processing.ms2denoise.window_width $data_processing.ms2denoise.relax"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
96 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
97
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
98 #if str($data_processing.ms2deisotope) == "true"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
99 --filter "MS2Deisotope"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
100 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
101
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
102
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
103 ## SCAN INCLUSION/EXCLUSION FILTERS
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
104 #if str($filtering.activation) != "false"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
105 --filter "activation $filtering.activation"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
106 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
107
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
108 #if len($filtering.indices) > 0
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
109 --filter "index
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
110 #for $index in $filtering.indices
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
111 [${index.from},${index.to}]
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
112 #end for
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
113 "
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
114 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
115
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
116 #if len($filtering.scan_numbers) > 0
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
117 --filter "scanNumber
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
118 #for $scan_number in $filtering.scan_numbers
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
119 [${scan_number.from},${scan_number.to}]
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
120 #end for
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
121 "
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
122 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
123
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
124 #if $filtering.strip_it.value
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
125 --filter "stripIT"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
126 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
127
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
128 #if $filtering.filter_ms_levels.do_ms_level_filter
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
129 --filter "msLevel [$filtering.filter_ms_levels.ms_level_from, $filtering.filter_ms_levels.ms_level_to]"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
130 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
131
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
132 #if str($filtering.polarity) != "false"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
133 --filter "polarity $filtering.polarity"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
134 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
135
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
136 #if str($filtering.analyzer) != "false"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
137 --filter "analyzer $filtering.analyzer"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
138 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
139
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
140 ## OUTPUT ENCODING
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
141 --
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
142 #set $mz_encoding = str($settings.mz_encoding)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
143 #set $intensity_encoding = str($settings.intensity_encoding)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
144 #if $mz_encoding == $intensity_encoding
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
145 #if $mz_encoding == "64"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
146 --64
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
147 #else
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
148 --32
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
149 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
150 #else
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
151 --mz${mz_encoding}
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
152 --inten${intensity_encoding}
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
153 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
154
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
155 #set binary_compression = str($settings.binary_compression)
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
156 #if $binary_compression == "zlib"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
157 --zlib
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
158 #else if $binary_compression == "numpressLinearPic"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
159 --numpressLinear --numpressPic
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
160 #else if $binary_compression == "numpressLinearSlof"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
161 --numpressLinear --numpressSlof
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
162 #else if $binary_compression == "numpressLinear"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
163 --numpressLinear
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
164 #else if $binary_compression == "numpressPic"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
165 --numpressPic
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
166 #else if $binary_compression == "numpressSlof"
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
167 --numpressSlof
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
168 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
169
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
170 #if $settings.gzip_compression
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
171 --gzip
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
172 #end if
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
173
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
174 ]]>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
175 </command>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
176 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
177
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
178 <xml name="msconvertInputParameters">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
179 <param name="output_type" type="select" label="Output Type">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
180 <option value="mz5" selected="true">mz5</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
181 <option value="mzML">mzML</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
182 <option value="mzXML">mzXML</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
183 <option value="mgf">mgf</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
184 <option value="ms2">ms2</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
185 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
186
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
187 <section name="data_processing" title="Data Processing Filters">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
188
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
189 <conditional name="peak_picking">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
190 <param type="boolean" name="pick_peaks" label="Apply peak picking?" truevalue="true" falsevalue="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
191 <when value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
192 <when value="true">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
193 <param name="pick_peaks_ms_levels" type="select" label="Peak Peaking - Apply to MS Levels">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
194 <option value="1">MS1 Only (1)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
195 <option value="2">MS2 Only (2)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
196 <option value="2-">MS2 and on (2-)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
197 <option value="1-" selected="true">All Levels (1-)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
198 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
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)">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
200 <option value="vendor" selected="true">Prefer vendor algorithm, fallback to local-maximum</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
201 <option value="cwt">CantWaiT - continuous wavelet transform</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
202 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
203 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
204 </conditional>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
205
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
206 <conditional name="precursor_refinement">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
207 <param type="boolean" name="use_mzrefinement" label="Apply m/z refinement with identification data?" truevalue="true" falsevalue="false" checked="False" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
208 <when value="false"></when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
209 <when value="true">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
210 <param name="input_ident" type="data" format="pepxml,mzid" label="MZRefinery - Input identification data" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
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+" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
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." />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
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)." />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
214 <param name="thresholdMaxSteps" type="integer" value="0" label="MZRefinery - At most, how many steps to widen the threshold?" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
215 <param name="precursor_refinement_ms_levels" type="select" label="MZRefinery - Apply to MS Levels">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
216 <option value="1">MS1 Only (1)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
217 <option value="2">MS2 Only (2)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
218 <option value="2-">MS2 and on (2-)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
219 <option value="1-" selected="true">All Levels (1-)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
220 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
221 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
222 </conditional>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
223
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
224 <conditional name="charge_state_calculation">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
225 <param name="charge_state_calculation_method" type="select" label="(Re-)calculate charge states?">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
226 <option value="false">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
227 <option value="predictor">Based on how much intensity is above vs. below the precursor m/z in the MS/MS scan</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
228 <option value="turbocharger">Based on isotopic distribution of the precursor in nearby survey scans</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
229 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
230 <when value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
231 <when value="predictor">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
232 <param name="predictor_overrideExistingCharge" type="boolean" label="Always override existing charge?" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
233 <param name="minMultipleCharge" type="integer" label="Minimum multiple charge state" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
234 <param name="maxMultipleCharge" type="integer" label="Maximum multiple charge state" value="3" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
235 <param name="singleChargeFractionTIC" type="float" label="Fraction of intensity below the precursor to be considered singly charged" max="1" min="0" value="0.9" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
236 <param name="maxKnownCharge" type="integer" label="Maximum charge allowed for &quot;known&quot; charges" help="This is applied even when not overriding existing charges (i.e. it overrides only obviously bogus charge states)" value="0" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
237 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
238 <when value="turbocharger">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
239 <param name="minCharge" type="integer" label="Minimum possible charge state" value="1" min="1" help="Charge states lower than this will not be considered." />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
240 <param name="maxCharge" type="integer" label="Maximum possible charge state" value="8" min="2" help="Charge states greater than this will not be considered." />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
241 <param name="precursorsBefore" type="integer" label="Number of preceding survey scans to check for precursor isotopes" value="2" min="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
242 <param name="precursorsAfter" type="integer" label="Number of succeeding survey scans to check for precursor isotopes" value="0" min="0" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
243 <param name="halfIsoWidth" type="float" label="Half-width of isolation window" min="0.0001" value="1.25" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
244 <param name="defaultMinCharge" type="integer" label="Minimum possible charge state to apply if no isotope is found" value="0" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
245 <param name="defaultMaxCharge" type="integer" label="Maximum possible charge state to apply if no isotope is found" value="0" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
246 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
247 </conditional>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
248
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
249 <repeat name="thresholds" title="Filter by Threshold">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
250 <param type="select" label="Specify threshold on" name="threshold_type" help="">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
251 <option value="count">Peak count</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
252 <option value="count-after-ties">Peak count (after ties)</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
253 <option value="absolute">Peak absolute intensity</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
254 <option value="bpi-relative">Fraction of base peak intensity</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
255 <option value="tic-relative">Fraction of total ion current</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
256 <option value="tic-fraction">Aggregate fraction of total ion current</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
257 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
258 <param type="float" name="value" label="Threshold" value="1" help="For count methods, this is the number of peaks to keep. For the absolute method, this is the raw intensity above/below which peak will be accepted. For the &quot;Aggregated fraction&quot; method, peaks are accepted until this fraction of the TIC is accounted for." />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
259 <param type="select" label="Keep" name="orientation">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
260 <option value="most-intense">Most intense peaks</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
261 <option value="least-intense">Least intense peaks</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
262 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
263 </repeat>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
264
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
265 <conditional name="filter_mz_windows">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
266 <param name="do_mzwindow_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
267 <when value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
268 <when value="true">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
269 <param name="mz_window_from" type="float" label="Filter m/z From" value="0.0" optional="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
270 <param name="mz_window_to" type="float" label="Filter m/z To" value="0.0" optional="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
271 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
272 </conditional>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
273
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
274 <conditional name="etd_filtering">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
275 <param type="boolean" name="do_etd_filtering" label="Filter out ETD precursor peaks?" truevalue="true" falsevalue="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
276 <when value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
277 <when value="true">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
278 <param name="remove_precursor" type="select" label="ETD Remove Unreacted Precursor">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
279 <option value="true" selected="true">yes</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
280 <option value="false">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
281 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
282 <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced Precursors">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
283 <option value="true" selected="true">yes</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
284 <option value="false">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
285 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
286 <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Losses" help="Remove neutral loss species from nominal and charge reduced precursors">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
287 <option value="true" selected="true">yes</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
288 <option value="false">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
289 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
290 <param name="blanket_removal" type="select" label="ETD Blanket Removal of Neutral Losses" help="Remove neutral losses in a charge-scaled 60 Da swath (rather than only around known loss species)">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
291 <option value="true" selected="true">yes</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
292 <option value="false">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
293 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
294 <param name="matching_tolerance" type="float" label="ETD Matching Tolerance" value="3.1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
295 <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
296 <option value="MZ" selected="true">mz</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
297 <option value="PPM">ppm</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
298 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
299 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
300 </conditional>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
301
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
302 <conditional name="ms2denoise">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
303 <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
304 <when value="true">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
305 <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
306 <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
307 <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
308 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
309 <when value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
310 </conditional>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
311
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
312 <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
313
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
314 </section>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
315
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
316
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
317 <section name="filtering" title="Scan Inclusion/Exclusion Filters">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
318
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
319 <param name="activation" type="select" label="Filter by Activation">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
320 <option value="false" selected="true">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
321 <option value="ETD">ETD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
322 <option value="CID">CID</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
323 <option value="SA">SA</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
324 <option value="HCD">HCD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
325 <option value="BIRD">BIRD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
326 <option value="ECD">ECD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
327 <option value="IRMPD">IRMPD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
328 <option value="PD">PD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
329 <option value="PSD">PSD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
330 <option value="PQD">PQD</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
331 <option value="SID">SID</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
332 <option value="SORI">SORI</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
333 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
334
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
335 <repeat name="indices" title="Filter Scan Indices">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
336 <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
337 <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
338 </repeat>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
339
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
340 <repeat name="scan_numbers" title="Filter Scan Numbers">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
341 <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
342 <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
343 </repeat>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
344
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
345 <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
346
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
347 <conditional name="filter_ms_levels">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
348 <param name="do_ms_level_filter" type="boolean" label="Filter MS Levels" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
349 <when value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
350 <when value="true">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
351 <param name="ms_level_from" type="integer" label="Filter MS Level From" value="0" optional="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
352 <param name="ms_level_to" type="integer" label="Filter MS Level To" value="0" optional="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
353 </when>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
354 </conditional>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
355
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
356 <param name="polarity" type="select" label="Filter by Polarity">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
357 <option value="false" selected="true">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
358 <option value="positive">positive</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
359 <option value="negative">negative</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
360 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
361
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
362 <param name="analyzer" type="select" label="Filter by Analyzer">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
363 <option value="false" selected="true">no</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
364 <option value="quad">Quadrupole</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
365 <option value="orbi">Orbitrap</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
366 <option value="FT">Fourier-transform</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
367 <option value="IT">Ion trap</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
368 <option value="TOF">Time of flight</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
369 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
370 </section>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
371
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
372
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
373 <section name="settings" title="Output Encoding Settings">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
374 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
375 <option value="64" selected="true">64</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
376 <option value="32">32</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
377 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
378 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
379 <option value="64">64</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
380 <option value="32" selected="true">32</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
381 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
382 <param type="select" name="binary_compression" label="Binary data compression">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
383 <option value="false">None</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
384 <option value="zlib" selected="true">zlib</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
385 <option value="numpressLinearPic">numpressLinear/numpressPic</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
386 <option value="numpressLinearSlof">numpressLinear/numpressSlof</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
387 <option value="numpressLinear">numpressLinear only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
388 <option value="numpressPic">numpressPic only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
389 <option value="numpressSlof">numpressSlof only</option>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
390 </param>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
391 <param type="boolean" name="gzip_compression" label="Compress output file with gzip" truevalue="true" falsevalue="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
392 </section>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
393 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
394
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
395 <xml name="msconvertOutput">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
396 <outputs>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
397 <data format="mzml" name="output" label="${input.name.rsplit('.',1)[0]}.${output_type}" >
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
398 <change_format>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
399 <when input="output_type" value="mz5" format="mz5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
400 <when input="output_type" value="mzXML" format="mzxml" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
401 <when input="output_type" value="ms2" format="ms2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
402 <when input="output_type" value="mgf" format="mgf" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
403 </change_format>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
404 </data>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
405 <data format="csv" name="output_refinement" label="${input.name.rsplit('.',1)[0]}.mzRefinement.tsv">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
406 <filter>data_processing['precursor_refinement']['use_mzrefinement'] == True</filter>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
407 </data>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
408 </outputs>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
409 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
410
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
411
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
412 <xml name="msconvert_tests">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
413 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
414 <param name="input" value="small.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
415 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
416 <param name="pick_peaks" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
417 <param name="pick_peaks_algorithm" value="cwt" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
418 <param name="pick_peaks_ms_levels" value="1-" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
419 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
420 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
421
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
422 <!-- this data file only has profile MS1, so the result is the same -->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
423 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
424 <param name="input" value="small.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
425 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
426 <param name="pick_peaks" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
427 <param name="pick_peaks_algorithm" value="cwt" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
428 <param name="pick_peaks_ms_levels" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
429 <output name="output" file="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
430 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
431 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
432 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
433 <param name="output_type" value="mz5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
434 <param name="mz_encoding" value="64" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
435 <param name="intensity_encoding" value="64" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
436 <output name="output" file="small-zlib-64.mz5" compare="sim_size" delta="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
437 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
438 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
439 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
440 <param name="output_type" value="mzXML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
441 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
442 <param name="intensity_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
443 <output name="output" file="small-zlib-32.mzXML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
444 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
445 <!-- TODO: how to test gzipped output?
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
446 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
447 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
448 <param name="output_type" value="mzXML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
449 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
450 <param name="intensity_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
451 <param name="binary_compression" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
452 <param name="gzip_compression" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
453 <output name="output" file="small-off-32.mzXML.gz" compare="sim_size" delta="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
454 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
455 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
456 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
457 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
458 <param name="mz_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
459 <param name="intensity_encoding" value="32" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
460 <param name="binary_compression" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
461 <param name="gzip_compression" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
462 <output name="output" file="small-off-32.mzML.gz" compare="sim_size" delta="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
463 </test>-->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
464
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
465 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
466 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
467 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
468 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
469 <output name="output" file="small-numpressLP.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
470 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
471
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
472 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
473 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
474 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
475 <param name="binary_compression" value="numpressLinearSlof" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
476 <output name="output" file="small-numpressLS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
477 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
478
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
479 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
480 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
481 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
482 <param name="binary_compression" value="numpressLinear" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
483 <output name="output" file="small-numpressL.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
484 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
485
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
486 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
487 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
488 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
489 <param name="binary_compression" value="numpressPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
490 <output name="output" file="small-numpressP.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
491 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
492
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
493 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
494 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
495 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
496 <param name="binary_compression" value="numpressSlof" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
497 <output name="output" file="small-numpressS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
498 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
499
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
500 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
501 <param name="input" value="Rpal_01.mz5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
502 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
503 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
504 <param name="use_mzrefinement" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
505 <param name="input_ident" value="Rpal_01.pepXML.gz" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
506 <param name="thresholdScore" value="mvh" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
507 <param name="thresholdValue" value="40-" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
508 <output name="output" file="Rpal_01-mzRefinement.mzML" compare="sim_size" delta="0" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
509 <output name="output.refinement" file="Rpal_01.pepXML.mzRefinement.tsv" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
510 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
511
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
512 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
513 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
514 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
515 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
516 <param name="charge_state_calculation_method" value="predictor" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
517 <param name="predictor_overrideExistingCharge" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
518 <param name="minMultipleCharge" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
519 <param name="maxMultipleCharge" value="5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
520 <param name="singleChargeFractionTIC" value="0.95" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
521 <param name="maxKnownCharge" value="8" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
522 <output name="output" file="small-chargeStatePredictor.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
523 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
524 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
525 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
526 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
527 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
528 <param name="charge_state_calculation_method" value="turbocharger" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
529 <param name="minCharge" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
530 <param name="maxCharge" value="5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
531 <param name="precursorsBefore" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
532 <param name="precursorsAfter" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
533 <param name="halfIsoWidth" value="1.5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
534 <param name="defaultMinCharge" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
535 <param name="defaultMaxCharge" value="5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
536 <output name="output" file="small-turbocharger.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
537 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
538 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
539 <param name="input" value="D100930_yeast_SCX10S_rak_ft8E_pc_01.mz5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
540 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
541 <param name="do_etd_filtering" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
542 <param name="remove_precursor" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
543 <param name="remove_charge_reduced" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
544 <param name="remove_neutral_loss" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
545 <param name="blanket_removal" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
546 <param name="matching_tolerance" value="50" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
547 <param name="matching_tolerance_units" value="ppm" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
548 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
549 <output name="output" file="D100930_yeast_SCX10S_rak_ft8E_pc_01-etdfilter.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
550 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
551 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
552 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
553 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
554 <param name="thresholds_0|threshold_type" value="count" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
555 <param name="thresholds_0|value" value="100" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
556 <param name="thresholds_0|orientation" value="most-intense" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
557 <param name="thresholds_1|threshold_type" value="absolute" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
558 <param name="thresholds_1|value" value="1" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
559 <param name="thresholds_1|orientation" value="most-intense" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
560 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
561 <output name="output" file="small-threshold.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
562 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
563 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
564 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
565 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
566 <param name="do_mzwindow_filter" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
567 <param name="mz_window_from" value="420" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
568 <param name="mz_window_to" value="840" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
569 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
570 <output name="output" file="small-mzWindow.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
571 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
572 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
573 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
574 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
575 <param name="denoise" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
576 <param name="num_peaks" value="10" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
577 <param name="window_width" value="40" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
578 <param name="relax" value="false" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
579 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
580 <output name="output" file="small-denoise.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
581 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
582 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
583 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
584 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
585 <param name="ms2deisotope" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
586 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
587 <output name="output" file="small-deisotope.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
588 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
589 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
590 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
591 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
592 <param name="activation" value="CID" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
593 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
594 <output name="output" file="small-activation.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
595 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
596 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
597 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
598 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
599 <param name="indices_0|from" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
600 <param name="indices_0|to" value="4" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
601 <param name="indices_1|from" value="10" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
602 <param name="indices_1|to" value="10" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
603 <param name="indices_2|from" value="13" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
604 <param name="indices_2|to" value="15" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
605 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
606 <output name="output" file="small-index-filter.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
607 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
608 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
609 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
610 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
611 <param name="strip_it" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
612 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
613 <output name="output" file="small-strip-it.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
614 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
615 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
616 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
617 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
618 <param name="do_ms_level_filter" value="true" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
619 <param name="ms_level_from" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
620 <param name="ms_level_to" value="2" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
621 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
622 <output name="output" file="small-ms-level-filter.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
623 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
624 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
625 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
626 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
627 <param name="polarity" value="positive" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
628 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
629 <output name="output" file="small-polarity-filter.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
630 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
631 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
632 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
633 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
634 <param name="analyzer" value="IT" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
635 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
636 <output name="output" file="small-analyzer-filter.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
637 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
638 <test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
639 <param name="input" value="small-peakpicking-cwt-allMS.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
640 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
641 <param name="scan_numbers_0|from" value="3" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
642 <param name="scan_numbers_0|to" value="5" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
643 <param name="scan_numbers_1|from" value="11" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
644 <param name="scan_numbers_1|to" value="11" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
645 <param name="scan_numbers_2|from" value="14" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
646 <param name="scan_numbers_2|to" value="16" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
647 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
648 <output name="output" file="small-index-filter.mzML" /> <!-- the scan numbers here produce the same output as the index test above -->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
649 </test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
650 <!--<test>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
651 <param name="input" value="small.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
652 <param name="output_type" value="mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
653 <param name="binary_compression" value="numpressLinearPic" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
654 <output name="output" file="small-deisotope-poisson.mzML" />
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
655 </test>-->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
656 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
657 <xml name="msconvert_help">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
658 **What it does**
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
659
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
660 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
661
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
662 You can view the original documentation here_.
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
663
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
664 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
665 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
666
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
667 <xml name="citations">
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
668 <citations>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
669 <citation type="doi">10.1093/bioinformatics/btn323</citation>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
670 <citation type="bibtex">@misc{toolsGalaxyP, author = {Chilton, J, Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
671 year = {2015}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = {$sha1$}" -->
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
672 </citations>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
673 </xml>
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
674
dd4ba10d0c45 planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
675 </macros>