Mercurial > repos > galaxyp > openms_masstraceextractor

comparison MassTraceExtractor.xml @ 1:cd7f683a669a 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 09:57:00 -0400
parents 2fdd110666cb
children 074f89bd9ec9
comparison
equal deleted inserted replaced
0:2fdd110666cb 1:cd7f683a669a
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="MassTraceExtractor" name="MassTraceExtractor" version="2.1.0"> 4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.2.0">
5 <description>Detects mass traces in centroided LC-MS data.</description> 5 <description>Detects mass traces in centroided LC-MS data.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MassTraceExtractor</token> 7 <token name="@EXECUTABLE@">MassTraceExtractor</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
37 #end if 37 #end if
38 #if $param_algorithm_mtd_mass_error_ppm: 38 #if $param_algorithm_mtd_mass_error_ppm:
39 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm 39 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
40 #end if 40 #end if
41 #if $param_algorithm_mtd_reestimate_mt_sd: 41 #if $param_algorithm_mtd_reestimate_mt_sd:
42 -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd 42 -algorithm:mtd:reestimate_mt_sd
43 #if " " in str($param_algorithm_mtd_reestimate_mt_sd):
44 "$param_algorithm_mtd_reestimate_mt_sd"
45 #else
46 $param_algorithm_mtd_reestimate_mt_sd
47 #end if
43 #end if 48 #end if
44 #if $param_algorithm_mtd_quant_method: 49 #if $param_algorithm_mtd_quant_method:
45 -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method 50 -algorithm:mtd:quant_method
51 #if " " in str($param_algorithm_mtd_quant_method):
52 "$param_algorithm_mtd_quant_method"
53 #else
54 $param_algorithm_mtd_quant_method
55 #end if
46 #end if 56 #end if
47 #if $param_algorithm_epd_width_filtering: 57 #if $param_algorithm_epd_width_filtering:
48 -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
49 #end if 64 #end if
50 #if $param_algorithm_epd_enabled: 65 #if $param_algorithm_epd_enabled:
51 -algorithm:epd:enabled $param_algorithm_epd_enabled 66 -algorithm:epd:enabled
67 #if " " in str($param_algorithm_epd_enabled):
68 "$param_algorithm_epd_enabled"
69 #else
70 $param_algorithm_epd_enabled
71 #end if
52 #end if 72 #end if
53 #if $adv_opts.adv_opts_selector=='advanced': 73 #if $adv_opts.adv_opts_selector=='advanced':
54 #if $adv_opts.param_force: 74 #if $adv_opts.param_force:
55 -force 75 -force
56 #end if 76 #end if
57 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: 77 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
58 -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion 78 -algorithm:mtd:trace_termination_criterion
79 #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
80 "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
81 #else
82 $adv_opts.param_algorithm_mtd_trace_termination_criterion
83 #end if
59 #end if 84 #end if
60 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: 85 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
61 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers 86 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
62 #end if 87 #end if
63 #if $adv_opts.param_algorithm_mtd_min_sample_rate: 88 #if $adv_opts.param_algorithm_mtd_min_sample_rate: