Mercurial > repos > galaxyp > openms_featurelinkerunlabeledqt

comparison FeatureLinkerUnlabeledQT.xml @ 3:b6739a31c49f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:10:00 -0400
parents 09d268b81f88
children 5e3b60ab2b05
comparison
equal deleted inserted replaced
2:0d277791c853 3:b6739a31c49f
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="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="2.1.0"> 4 <tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" 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@">FeatureLinkerUnlabeledQT</token> 7 <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</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>
78 </valid> 86 </valid>
79 </sanitizer> 87 </sanitizer>
80 </param> 88 </param>
81 <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/> 89 <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
82 <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help="(-use_identifications) "/> 90 <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help="(-use_identifications) "/>
83 <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="1" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" help="(-nr_partitions) "/> 91 <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" help="(-nr_partitions) "/>
84 <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/> 92 <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
85 <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/> 93 <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
86 <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/> 94 <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
87 <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) "> 95 <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) ">
88 <option value="Da" selected="true">Da</option> 96 <option value="Da" selected="true">Da</option>
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>