Mercurial > repos > galaxyp > openms_featurefindermetabo

comparison FeatureFinderMetabo.xml @ 1:15cc4acac8c3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 16:04:46 -0400
parents 2602a6da5ad3
children 514ecafed38f
comparison
equal deleted inserted replaced
0:2602a6da5ad3 1:15cc4acac8c3
29 #end if 29 #end if
30 #if $param_algorithm_mtd_mass_error_ppm: 30 #if $param_algorithm_mtd_mass_error_ppm:
31 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm 31 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
32 #end if 32 #end if
33 #if $param_algorithm_mtd_reestimate_mt_sd: 33 #if $param_algorithm_mtd_reestimate_mt_sd:
34 -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd 34 -algorithm:mtd:reestimate_mt_sd
35 #if " " in str($param_algorithm_mtd_reestimate_mt_sd):
36 "$param_algorithm_mtd_reestimate_mt_sd"
37 #else
38 $param_algorithm_mtd_reestimate_mt_sd
39 #end if
35 #end if 40 #end if
36 #if $param_algorithm_mtd_quant_method: 41 #if $param_algorithm_mtd_quant_method:
37 -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method 42 -algorithm:mtd:quant_method
43 #if " " in str($param_algorithm_mtd_quant_method):
44 "$param_algorithm_mtd_quant_method"
45 #else
46 $param_algorithm_mtd_quant_method
47 #end if
38 #end if 48 #end if
39 #if $param_algorithm_epd_enabled: 49 #if $param_algorithm_epd_enabled:
40 -algorithm:epd:enabled $param_algorithm_epd_enabled 50 -algorithm:epd:enabled
51 #if " " in str($param_algorithm_epd_enabled):
52 "$param_algorithm_epd_enabled"
53 #else
54 $param_algorithm_epd_enabled
55 #end if
41 #end if 56 #end if
42 #if $param_algorithm_epd_width_filtering: 57 #if $param_algorithm_epd_width_filtering:
43 -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering 58 -algorithm:epd:width_filtering
59 #if " " in str($param_algorithm_epd_width_filtering):
60 "$param_algorithm_epd_width_filtering"
61 #else
62 $param_algorithm_epd_width_filtering
63 #end if
44 #end if 64 #end if
45 #if $param_algorithm_ffm_charge_lower_bound: 65 #if $param_algorithm_ffm_charge_lower_bound:
46 -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound 66 -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound
47 #end if 67 #end if
48 #if $param_algorithm_ffm_charge_upper_bound: 68 #if $param_algorithm_ffm_charge_upper_bound:
49 -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound 69 -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound
50 #end if 70 #end if
51 #if $param_algorithm_ffm_enable_RT_filtering: 71 #if $param_algorithm_ffm_enable_RT_filtering:
52 -algorithm:ffm:enable_RT_filtering $param_algorithm_ffm_enable_RT_filtering 72 -algorithm:ffm:enable_RT_filtering
73 #if " " in str($param_algorithm_ffm_enable_RT_filtering):
74 "$param_algorithm_ffm_enable_RT_filtering"
75 #else
76 $param_algorithm_ffm_enable_RT_filtering
77 #end if
53 #end if 78 #end if
54 #if $param_algorithm_ffm_isotope_filtering_model: 79 #if $param_algorithm_ffm_isotope_filtering_model:
55 -algorithm:ffm:isotope_filtering_model $param_algorithm_ffm_isotope_filtering_model 80 -algorithm:ffm:isotope_filtering_model
81 #if " " in str($param_algorithm_ffm_isotope_filtering_model):
82 "$param_algorithm_ffm_isotope_filtering_model"
83 #else
84 $param_algorithm_ffm_isotope_filtering_model
85 #end if
56 #end if 86 #end if
57 #if $param_algorithm_ffm_mz_scoring_13C: 87 #if $param_algorithm_ffm_mz_scoring_13C:
58 -algorithm:ffm:mz_scoring_13C 88 -algorithm:ffm:mz_scoring_13C
59 #end if 89 #end if
60 #if $param_algorithm_ffm_report_convex_hulls: 90 #if $param_algorithm_ffm_report_convex_hulls:
63 #if $adv_opts.adv_opts_selector=='advanced': 93 #if $adv_opts.adv_opts_selector=='advanced':
64 #if $adv_opts.param_force: 94 #if $adv_opts.param_force:
65 -force 95 -force
66 #end if 96 #end if
67 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: 97 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
68 -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion 98 -algorithm:mtd:trace_termination_criterion
99 #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
100 "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
101 #else
102 $adv_opts.param_algorithm_mtd_trace_termination_criterion
103 #end if
69 #end if 104 #end if
70 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: 105 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
71 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers 106 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
72 #end if 107 #end if
73 #if $adv_opts.param_algorithm_mtd_min_sample_rate: 108 #if $adv_opts.param_algorithm_mtd_min_sample_rate:
96 #end if 131 #end if
97 #if $adv_opts.param_algorithm_ffm_report_summed_ints: 132 #if $adv_opts.param_algorithm_ffm_report_summed_ints:
98 -algorithm:ffm:report_summed_ints 133 -algorithm:ffm:report_summed_ints
99 #end if 134 #end if
100 #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities: 135 #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities:
101 -algorithm:ffm:use_smoothed_intensities $adv_opts.param_algorithm_ffm_use_smoothed_intensities 136 -algorithm:ffm:use_smoothed_intensities
137 #if " " in str($adv_opts.param_algorithm_ffm_use_smoothed_intensities):
138 "$adv_opts.param_algorithm_ffm_use_smoothed_intensities"
139 #else
140 $adv_opts.param_algorithm_ffm_use_smoothed_intensities
141 #end if
102 #end if 142 #end if
103 #end if 143 #end if
104 </command> 144 </command>
105 <inputs> 145 <inputs>
106 <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/> 146 <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>