Mercurial > repos > galaxyp > openms_maprttransformer

comparison MapRTTransformer.xml @ 1:af8d0e751415 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 09:08:09 -0400
parents 652ee76d7113
children 5b776e2133f1
comparison
equal deleted inserted replaced
0:652ee76d7113 1:af8d0e751415
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="MapRTTransformer" name="MapRTTransformer" version="2.1.0"> 4 <tool id="MapRTTransformer" name="MapRTTransformer" version="2.2.0">
5 <description>Applies retention time transformations to maps.</description> 5 <description>Applies retention time transformations to maps.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapRTTransformer</token> 7 <token name="@EXECUTABLE@">MapRTTransformer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
29 #end if 29 #end if
30 #if $param_store_original_rt: 30 #if $param_store_original_rt:
31 -store_original_rt 31 -store_original_rt
32 #end if 32 #end if
33 #if $param_model_type: 33 #if $param_model_type:
34 -model:type $param_model_type 34 -model:type
35 #if " " in str($param_model_type):
36 "$param_model_type"
37 #else
38 $param_model_type
39 #end if
35 #end if 40 #end if
36 #if $param_model_linear_symmetric_regression: 41 #if $param_model_linear_symmetric_regression:
37 -model:linear:symmetric_regression 42 -model:linear:symmetric_regression
38 #end if 43 #end if
39 #if $param_model_b_spline_wavelength: 44 #if $param_model_b_spline_wavelength:
41 #end if 46 #end if
42 #if $param_model_b_spline_num_nodes: 47 #if $param_model_b_spline_num_nodes:
43 -model:b_spline:num_nodes $param_model_b_spline_num_nodes 48 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
44 #end if 49 #end if
45 #if $param_model_b_spline_extrapolate: 50 #if $param_model_b_spline_extrapolate:
46 -model:b_spline:extrapolate $param_model_b_spline_extrapolate 51 -model:b_spline:extrapolate
52 #if " " in str($param_model_b_spline_extrapolate):
53 "$param_model_b_spline_extrapolate"
54 #else
55 $param_model_b_spline_extrapolate
56 #end if
47 #end if 57 #end if
48 #if $param_model_b_spline_boundary_condition: 58 #if $param_model_b_spline_boundary_condition:
49 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition 59 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
50 #end if 60 #end if
51 #if $param_model_lowess_span: 61 #if $param_model_lowess_span:
56 #end if 66 #end if
57 #if $param_model_lowess_delta: 67 #if $param_model_lowess_delta:
58 -model:lowess:delta $param_model_lowess_delta 68 -model:lowess:delta $param_model_lowess_delta
59 #end if 69 #end if
60 #if $param_model_lowess_interpolation_type: 70 #if $param_model_lowess_interpolation_type:
61 -model:lowess:interpolation_type $param_model_lowess_interpolation_type 71 -model:lowess:interpolation_type
72 #if " " in str($param_model_lowess_interpolation_type):
73 "$param_model_lowess_interpolation_type"
74 #else
75 $param_model_lowess_interpolation_type
76 #end if
62 #end if 77 #end if
63 #if $param_model_lowess_extrapolation_type: 78 #if $param_model_lowess_extrapolation_type:
64 -model:lowess:extrapolation_type $param_model_lowess_extrapolation_type 79 -model:lowess:extrapolation_type
80 #if " " in str($param_model_lowess_extrapolation_type):
81 "$param_model_lowess_extrapolation_type"
82 #else
83 $param_model_lowess_extrapolation_type
84 #end if
65 #end if 85 #end if
66 #if $param_model_interpolated_interpolation_type: 86 #if $param_model_interpolated_interpolation_type:
67 -model:interpolated:interpolation_type $param_model_interpolated_interpolation_type 87 -model:interpolated:interpolation_type
88 #if " " in str($param_model_interpolated_interpolation_type):
89 "$param_model_interpolated_interpolation_type"
90 #else
91 $param_model_interpolated_interpolation_type
92 #end if
68 #end if 93 #end if
69 #if $param_model_interpolated_extrapolation_type: 94 #if $param_model_interpolated_extrapolation_type:
70 -model:interpolated:extrapolation_type $param_model_interpolated_extrapolation_type 95 -model:interpolated:extrapolation_type
96 #if " " in str($param_model_interpolated_extrapolation_type):
97 "$param_model_interpolated_extrapolation_type"
98 #else
99 $param_model_interpolated_extrapolation_type
100 #end if
71 #end if 101 #end if
72 #if $adv_opts.adv_opts_selector=='advanced': 102 #if $adv_opts.adv_opts_selector=='advanced':
73 #if $adv_opts.param_force: 103 #if $adv_opts.param_force:
74 -force 104 -force
75 #end if 105 #end if
76 #end if 106 #end if
77 </command> 107 </command>
78 <inputs> 108 <inputs>
79 <param name="param_in" type="data" format="featurexml,consensusxml,mzml,idxml" optional="True" label="Input file to transform (separated by blanks)" help="(-in) "/> 109 <param name="param_in" type="data" format="mzml,featurexml,consensusxml,idxml" optional="True" label="Input file to transform (separated by blanks)" help="(-in) "/>
80 <param name="param_trafo_in" type="data" format="trafoxml" optional="False" label="Transformation to apply" help="(-trafo_in) "/> 110 <param name="param_trafo_in" type="data" format="trafoxml" optional="False" label="Transformation to apply" help="(-trafo_in) "/>
81 <param name="param_invert" display="radio" type="boolean" truevalue="-invert" falsevalue="" checked="false" optional="True" label="Invert transformation (approximatively) before applying it" help="(-invert) "/> 111 <param name="param_invert" display="radio" type="boolean" truevalue="-invert" falsevalue="" checked="false" optional="True" label="Invert transformation (approximatively) before applying it" help="(-invert) "/>
82 <param name="param_store_original_rt" display="radio" type="boolean" truevalue="-store_original_rt" falsevalue="" checked="false" optional="True" label="Store the original retention times (before transformation) as meta data in the output file" help="(-store_original_rt) "/> 112 <param name="param_store_original_rt" display="radio" type="boolean" truevalue="-store_original_rt" falsevalue="" checked="false" optional="True" label="Store the original retention times (before transformation) as meta data in the output file" help="(-store_original_rt) "/>
83 <param name="param_model_type" type="select" optional="False" value="none" label="Type of model" help="(-type) "> 113 <param name="param_model_type" type="select" optional="False" value="none" label="Type of model" help="(-type) ">
84 <option value="none" selected="true">none</option> 114 <option value="none" selected="true">none</option>