Mercurial > repos > galaxyp > openms_tofcalibration
annotate TOFCalibration.xml @ 0:5e6e9b779e4d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:30:10 -0500 |
| parents | |
| children | 9e45515b43d6 |
| rev | line source |
|---|---|
|
0
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
1 <?xml version='1.0' encoding='UTF-8'?> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
4 <tool id="TOFCalibration" name="TOFCalibration" version="2.1.0"> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
5 <description>Applies time of flight calibration.</description> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
6 <macros> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
7 <token name="@EXECUTABLE@">TOFCalibration</token> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
8 <import>macros.xml</import> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
9 </macros> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
10 <expand macro="references"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
11 <expand macro="stdio"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
12 <expand macro="requirements"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
13 <command>TOFCalibration |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
14 |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
15 #if $param_in: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
16 -in $param_in |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
17 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
18 #if $param_out: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
19 -out $param_out |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
20 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
21 #if $param_ext_calibrants: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
22 -ext_calibrants $param_ext_calibrants |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
23 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
24 #if $param_ref_masses: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
25 -ref_masses $param_ref_masses |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
26 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
27 #if $param_tof_const: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
28 -tof_const $param_tof_const |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
29 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
30 #if $param_peak_data: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
31 -peak_data |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
32 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
33 #if $param_algorithm_PeakPicker_signal_to_noise: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
34 -algorithm:PeakPicker:signal_to_noise $param_algorithm_PeakPicker_signal_to_noise |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
35 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
36 #if $param_algorithm_PeakPicker_peak_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
37 -algorithm:PeakPicker:peak_width $param_algorithm_PeakPicker_peak_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
38 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
39 #if $param_algorithm_PeakPicker_estimate_peak_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
40 -algorithm:PeakPicker:estimate_peak_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
41 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
42 #if $adv_opts.adv_opts_selector=='advanced': |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
43 #if $adv_opts.param_force: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
44 -force |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
45 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
46 #if $adv_opts.param_algorithm_PeakPicker_centroid_percentage: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
47 -algorithm:PeakPicker:centroid_percentage $adv_opts.param_algorithm_PeakPicker_centroid_percentage |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
48 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
49 #if $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
50 -algorithm:PeakPicker:fwhm_lower_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
51 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
52 #if $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
53 -algorithm:PeakPicker:fwhm_upper_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
54 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
55 #if $adv_opts.param_algorithm_PeakPicker_optimization_iterations: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
56 -algorithm:PeakPicker:optimization:iterations $adv_opts.param_algorithm_PeakPicker_optimization_iterations |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
57 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
58 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
59 -algorithm:PeakPicker:optimization:penalties:position $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
60 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
61 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
62 -algorithm:PeakPicker:optimization:penalties:left_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
63 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
64 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
65 -algorithm:PeakPicker:optimization:penalties:right_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
66 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
67 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
68 -algorithm:PeakPicker:optimization:penalties:height $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
69 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
70 #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
71 -algorithm:PeakPicker:optimization:2d:tolerance_mz $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
72 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
73 #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
74 -algorithm:PeakPicker:optimization:2d:max_peak_distance $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
75 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
76 #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
77 -algorithm:PeakPicker:thresholds:peak_bound $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
78 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
79 #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
80 -algorithm:PeakPicker:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
81 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
82 #if $adv_opts.param_algorithm_PeakPicker_thresholds_correlation: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
83 -algorithm:PeakPicker:thresholds:correlation $adv_opts.param_algorithm_PeakPicker_thresholds_correlation |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
84 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
85 #if $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
86 -algorithm:PeakPicker:thresholds:noise_level $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
87 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
88 #if $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
89 -algorithm:PeakPicker:thresholds:search_radius $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
90 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
91 #if $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
92 -algorithm:PeakPicker:wavelet_transform:spacing $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
93 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
94 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_deconvolution: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
95 -algorithm:PeakPicker:deconvolution:deconvolution |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
96 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
97 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
98 -algorithm:PeakPicker:deconvolution:asym_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
99 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
100 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
101 -algorithm:PeakPicker:deconvolution:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
102 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
103 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
104 -algorithm:PeakPicker:deconvolution:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
105 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
106 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
107 -algorithm:PeakPicker:deconvolution:scaling $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
108 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
109 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
110 -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
111 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
112 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
113 -algorithm:PeakPicker:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
114 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
115 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
116 -algorithm:PeakPicker:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
117 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
118 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
119 -algorithm:PeakPicker:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
120 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
121 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
122 -algorithm:PeakPicker:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
123 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
124 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
125 -algorithm:PeakPicker:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
126 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
127 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
128 -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
129 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
130 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
131 -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
132 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
133 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
134 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
135 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
136 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
137 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
138 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
139 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
140 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
141 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
142 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
143 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
144 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
145 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
146 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
147 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
148 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
149 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
150 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
151 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
152 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
153 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
154 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
155 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
156 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
157 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window: |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
158 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
159 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
160 #end if |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
161 </command> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
162 <inputs> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
163 <param name="param_in" type="data" format="mzml" optional="False" label="input peak or raw data file" help="(-in) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
164 <param name="param_ext_calibrants" type="data" format="mzml" optional="False" label="input file containing the external calibrant spectra (peak or raw data)" help="(-ext_calibrants) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
165 <param name="param_ref_masses" type="data" format="txt" optional="False" label="input file containing reference masses of the external calibrant spectra (one per line)" help="(-ref_masses) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
166 <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants" help="(-tof_const) These can be either two or three constants <br>per set, depending on the conversion type. Either one set for all calibrant spectra <br>(tab separated), or one for each spectrum. <br>For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
167 <param name="param_peak_data" display="radio" type="boolean" truevalue="-peak_data" falsevalue="" checked="false" optional="True" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help="(-peak_data) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
168 <param name="param_algorithm_PeakPicker_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help="(-signal_to_noise) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
169 <param name="param_algorithm_PeakPicker_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks" help="(-peak_width) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
170 <param name="param_algorithm_PeakPicker_estimate_peak_width" display="radio" type="boolean" truevalue="-algorithm:PeakPicker:estimate_peak_width" falsevalue="" checked="false" optional="True" label="Flag if the average peak width shall be estimated" help="(-estimate_peak_width) Attention: when this flag is set, the peak_width is ignored"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
171 <expand macro="advanced_options"> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
172 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
173 <param name="param_algorithm_PeakPicker_centroid_percentage" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="(-centroid_percentage) If it is 1 the centroid position corresponds to the position of the highest intensity"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
174 <param name="param_algorithm_PeakPicker_fwhm_lower_bound_factor" type="float" min="0.0" optional="True" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="(-fwhm_lower_bound_factor) All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
175 <param name="param_algorithm_PeakPicker_fwhm_upper_bound_factor" type="float" min="0.0" optional="True" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="(-fwhm_upper_bound_factor) All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
176 <param name="param_algorithm_PeakPicker_optimization_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
177 <param name="param_algorithm_PeakPicker_optimization_penalties_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help="(-position) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
178 <param name="param_algorithm_PeakPicker_optimization_penalties_left_width" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help="(-left_width) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
179 <param name="param_algorithm_PeakPicker_optimization_penalties_right_width" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help="(-right_width) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
180 <param name="param_algorithm_PeakPicker_optimization_penalties_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help="(-height) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
181 <param name="param_algorithm_PeakPicker_optimization_2d_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
182 <param name="param_algorithm_PeakPicker_optimization_2d_max_peak_distance" type="float" min="0.0" optional="True" value="1.2" label="maximal peak distance in mz in a cluste" help="(-max_peak_distance) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
183 <param name="param_algorithm_PeakPicker_thresholds_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity" help="(-peak_bound) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
184 <param name="param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity for MS/MS peaks" help="(-peak_bound_ms2_level) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
185 <param name="param_algorithm_PeakPicker_thresholds_correlation" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="minimal correlation of a peak and the raw signal" help="(-correlation) If a peak has a lower correlation it is skipped"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
186 <param name="param_algorithm_PeakPicker_thresholds_noise_level" type="float" min="0.0" optional="True" value="0.1" label="noise level for the search of the peak endpoints" help="(-noise_level) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
187 <param name="param_algorithm_PeakPicker_thresholds_search_radius" type="integer" min="0" optional="True" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help="(-search_radius) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
188 <param name="param_algorithm_PeakPicker_wavelet_transform_spacing" type="float" min="0.0" optional="True" value="0.001" label="Spacing of the CWT" help="(-spacing) Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
189 <param name="param_algorithm_PeakPicker_deconvolution_deconvolution" display="radio" type="boolean" truevalue="-algorithm:PeakPicker:deconvolution:deconvolution" falsevalue="" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to "true"" help="(-deconvolution) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
190 <param name="param_algorithm_PeakPicker_deconvolution_asym_threshold" type="float" min="0.0" optional="True" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help="(-asym_threshold) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
191 <param name="param_algorithm_PeakPicker_deconvolution_left_width" type="float" min="0.0" optional="True" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help="(-left_width) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
192 <param name="param_algorithm_PeakPicker_deconvolution_right_width" type="float" min="0.0" optional="True" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help="(-right_width) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
193 <param name="param_algorithm_PeakPicker_deconvolution_scaling" type="float" min="0.0" optional="True" value="0.12" label="Initial scaling of the cwt used in the separation of heavily overlapping peaks" help="(-scaling) The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
194 <param name="param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold" type="float" min="0.0" optional="True" value="0.7" label="If the FWHM of a peak is higher than 'fwhm_thresholds' it is assumed that it consists of more than one peak and the deconvolution procedure is started" help="(-fwhm_threshold) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
195 <param name="param_algorithm_PeakPicker_deconvolution_fitting_eps_abs" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help="(-eps_abs) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
196 <param name="param_algorithm_PeakPicker_deconvolution_fitting_eps_rel" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the relative error gets smaller than this value the fitting is stopped" help="(-eps_rel) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
197 <param name="param_algorithm_PeakPicker_deconvolution_fitting_max_iteration" type="integer" min="1" optional="True" value="10" label="maximal number of iterations for the fitting step" help="(-max_iteration) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
198 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help="(-position) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
199 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help="(-height) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
200 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help="(-left_width) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
201 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help="(-right_width) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
202 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
203 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
204 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
205 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
206 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
207 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
208 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp" type="float" min="0.01" max="999.0" optional="True" value="3.0" label="multiplier for stdev" help="(-stdev_mp) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
209 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
210 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
211 </expand> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
212 </inputs> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
213 <outputs> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
214 <data name="param_out" format="mzml"/> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
215 </outputs> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
216 <help>Applies time of flight calibration. |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
217 |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
218 |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
219 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html</help> |
|
5e6e9b779e4d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff
changeset
|
220 </tool> |