Mercurial > repos > galaxyp > openms_featurelinkerunlabeled
comparison FeatureLinkerUnlabeled.xml @ 3:d21258431e2a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 09 Aug 2017 09:57:53 -0400 |
parents | fad4af2df6a4 |
children | df7f4ac9a2c6 |
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2:2fbd9dde16fa | 3:d21258431e2a |
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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: [Map Alignment]--> | 3 <!--Proposed Tool Section: [Map Alignment]--> |
4 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.1.0"> | 4 <tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.2.0"> |
5 <description>Groups corresponding features from multiple maps.</description> | 5 <description>Groups corresponding features from multiple maps.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token> | 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 </macros> | 9 </macros> |
65 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent | 65 -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent |
66 #end if | 66 #end if |
67 #if $adv_opts.param_algorithm_distance_intensity_weight: | 67 #if $adv_opts.param_algorithm_distance_intensity_weight: |
68 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight | 68 -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight |
69 #end if | 69 #end if |
70 #if $adv_opts.param_algorithm_distance_intensity_log_transform: | |
71 -algorithm:distance_intensity:log_transform | |
72 #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform): | |
73 "$adv_opts.param_algorithm_distance_intensity_log_transform" | |
74 #else | |
75 $adv_opts.param_algorithm_distance_intensity_log_transform | |
76 #end if | |
77 #end if | |
70 #end if | 78 #end if |
71 </command> | 79 </command> |
72 <inputs> | 80 <inputs> |
73 <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) "> | 81 <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) "> |
74 <sanitizer> | 82 <sanitizer> |
94 <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> | 102 <param name="param_algorithm_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> |
95 <param name="param_algorithm_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> | 103 <param name="param_algorithm_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> |
96 <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/> | 104 <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/> |
97 <param name="param_algorithm_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> | 105 <param name="param_algorithm_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> |
98 <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/> | 106 <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/> |
107 <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> | |
108 <option value="enabled">enabled</option> | |
109 <option value="disabled" selected="true">disabled</option> | |
110 </param> | |
99 </expand> | 111 </expand> |
100 </inputs> | 112 </inputs> |
101 <outputs> | 113 <outputs> |
102 <data name="param_out" format="consensusxml"/> | 114 <data name="param_out" format="consensusxml"/> |
103 </outputs> | 115 </outputs> |