Mercurial > repos > galaxyp > openms_spectramerger

comparison SpectraMerger.xml @ 1:4a91d040aa01 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:35:00 -0400
parents 899812f5c032
children 5b8e882b9fdc
comparison
equal deleted inserted replaced
0:899812f5c032 1:4a91d040aa01
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="SpectraMerger" name="SpectraMerger" version="2.1.0"> 4 <tool id="SpectraMerger" name="SpectraMerger" version="2.2.0">
5 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description> 5 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SpectraMerger</token> 7 <token name="@EXECUTABLE@">SpectraMerger</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
19 -out $param_out 19 -out $param_out
20 #end if 20 #end if
21 #if $param_merging_method: 21 #if $param_merging_method:
22 -merging_method $param_merging_method 22 -merging_method
23 #if " " in str($param_merging_method):
24 "$param_merging_method"
25 #else
26 $param_merging_method
27 #end if
23 #end if 28 #end if
24 #if $param_algorithm_average_gaussian_spectrum_type: 29 #if $param_algorithm_average_gaussian_spectrum_type:
25 -algorithm:average_gaussian:spectrum_type $param_algorithm_average_gaussian_spectrum_type 30 -algorithm:average_gaussian:spectrum_type
31 #if " " in str($param_algorithm_average_gaussian_spectrum_type):
32 "$param_algorithm_average_gaussian_spectrum_type"
33 #else
34 $param_algorithm_average_gaussian_spectrum_type
35 #end if
26 #end if 36 #end if
27 #if $param_algorithm_average_gaussian_ms_level: 37 #if $param_algorithm_average_gaussian_ms_level:
28 -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level 38 -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
29 #end if 39 #end if
30 #if $param_algorithm_average_gaussian_rt_FWHM: 40 #if $param_algorithm_average_gaussian_rt_FWHM:
31 -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM 41 -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
32 #end if 42 #end if
33 #if $param_algorithm_average_tophat_spectrum_type: 43 #if $param_algorithm_average_tophat_spectrum_type:
34 -algorithm:average_tophat:spectrum_type $param_algorithm_average_tophat_spectrum_type 44 -algorithm:average_tophat:spectrum_type
45 #if " " in str($param_algorithm_average_tophat_spectrum_type):
46 "$param_algorithm_average_tophat_spectrum_type"
47 #else
48 $param_algorithm_average_tophat_spectrum_type
49 #end if
35 #end if 50 #end if
36 #if $param_algorithm_average_tophat_ms_level: 51 #if $param_algorithm_average_tophat_ms_level:
37 -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level 52 -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
38 #end if 53 #end if
39 #if $param_algorithm_average_tophat_rt_range: 54 #if $param_algorithm_average_tophat_rt_range:
40 -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range 55 -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
41 #end if 56 #end if
42 #if $param_algorithm_average_tophat_rt_unit: 57 #if $param_algorithm_average_tophat_rt_unit:
43 -algorithm:average_tophat:rt_unit $param_algorithm_average_tophat_rt_unit 58 -algorithm:average_tophat:rt_unit
59 #if " " in str($param_algorithm_average_tophat_rt_unit):
60 "$param_algorithm_average_tophat_rt_unit"
61 #else
62 $param_algorithm_average_tophat_rt_unit
63 #end if
44 #end if 64 #end if
45 65
46 #if $rep_param_algorithm_block_method_ms_levels: 66 #if $rep_param_algorithm_block_method_ms_levels:
47 -algorithm:block_method:ms_levels 67 -algorithm:block_method:ms_levels
48 #for token in $rep_param_algorithm_block_method_ms_levels: 68 #for token in $rep_param_algorithm_block_method_ms_levels:
71 #end if 91 #end if
72 #if $adv_opts.param_algorithm_mz_binning_width: 92 #if $adv_opts.param_algorithm_mz_binning_width:
73 -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width 93 -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
74 #end if 94 #end if
75 #if $adv_opts.param_algorithm_mz_binning_width_unit: 95 #if $adv_opts.param_algorithm_mz_binning_width_unit:
76 -algorithm:mz_binning_width_unit $adv_opts.param_algorithm_mz_binning_width_unit 96 -algorithm:mz_binning_width_unit
97 #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit):
98 "$adv_opts.param_algorithm_mz_binning_width_unit"
99 #else
100 $adv_opts.param_algorithm_mz_binning_width_unit
101 #end if
77 #end if 102 #end if
78 #if $adv_opts.param_algorithm_sort_blocks: 103 #if $adv_opts.param_algorithm_sort_blocks:
79 -algorithm:sort_blocks $adv_opts.param_algorithm_sort_blocks 104 -algorithm:sort_blocks
105 #if " " in str($adv_opts.param_algorithm_sort_blocks):
106 "$adv_opts.param_algorithm_sort_blocks"
107 #else
108 $adv_opts.param_algorithm_sort_blocks
109 #end if
80 #end if 110 #end if
81 #if $adv_opts.param_algorithm_average_gaussian_cutoff: 111 #if $adv_opts.param_algorithm_average_gaussian_cutoff:
82 -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff 112 -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff
83 #end if 113 #end if
84 #end if 114 #end if