|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="MapRTTransformer" name="MapRTTransformer" version="2.0.0">
|
|
|
3 <description>Applies retention time transformations to maps.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">MapRTTransformer</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>MapRTTransformer
|
|
|
11
|
|
|
12 -in
|
|
|
13 #for token in $param_in:
|
|
|
14 $token
|
|
|
15 #end for
|
|
|
16
|
|
|
17 #if $rep_param_out:
|
|
|
18 -out
|
|
|
19 #for token in $rep_param_out:
|
|
|
20 #if " " in str(token):
|
|
|
21 "$token.param_out"
|
|
|
22 #else
|
|
|
23 $token.param_out
|
|
|
24 #end if
|
|
|
25 #end for
|
|
|
26 #end if
|
|
|
27 -trafo_in
|
|
|
28 #for token in $param_trafo_in:
|
|
|
29 $token
|
|
|
30 #end for
|
|
|
31
|
|
|
32 #if $rep_param_trafo_out:
|
|
|
33 -trafo_out
|
|
|
34 #for token in $rep_param_trafo_out:
|
|
|
35 #if " " in str(token):
|
|
|
36 "$token.param_trafo_out"
|
|
|
37 #else
|
|
|
38 $token.param_trafo_out
|
|
|
39 #end if
|
|
|
40 #end for
|
|
|
41 #end if
|
|
|
42 #if $param_invert:
|
|
|
43 -invert
|
|
|
44 #end if
|
|
|
45 -threads \${GALAXY_SLOTS:-24}
|
|
|
46 #if $param_model_type:
|
|
|
47 -model:type
|
|
|
48 #if " " in str($param_model_type):
|
|
|
49 "$param_model_type"
|
|
|
50 #else
|
|
|
51 $param_model_type
|
|
|
52 #end if
|
|
|
53 #end if
|
|
|
54 #if $param_model_linear_symmetric_regression:
|
|
|
55 -model:linear:symmetric_regression
|
|
|
56 #end if
|
|
|
57 #if $param_model_b_spline_wavelength:
|
|
|
58 -model:b_spline:wavelength $param_model_b_spline_wavelength
|
|
|
59 #end if
|
|
|
60 #if $param_model_b_spline_num_nodes:
|
|
|
61 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
|
|
|
62 #end if
|
|
|
63 #if $param_model_b_spline_extrapolate:
|
|
|
64 -model:b_spline:extrapolate
|
|
|
65 #if " " in str($param_model_b_spline_extrapolate):
|
|
|
66 "$param_model_b_spline_extrapolate"
|
|
|
67 #else
|
|
|
68 $param_model_b_spline_extrapolate
|
|
|
69 #end if
|
|
|
70 #end if
|
|
|
71 #if $param_model_b_spline_boundary_condition:
|
|
|
72 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
|
|
|
73 #end if
|
|
|
74 #if $param_model_interpolated_interpolation_type:
|
|
|
75 -model:interpolated:interpolation_type
|
|
|
76 #if " " in str($param_model_interpolated_interpolation_type):
|
|
|
77 "$param_model_interpolated_interpolation_type"
|
|
|
78 #else
|
|
|
79 $param_model_interpolated_interpolation_type
|
|
|
80 #end if
|
|
|
81 #end if
|
|
|
82 #if $adv_opts.adv_opts_selector=='advanced':
|
|
|
83 #if $adv_opts.param_force:
|
|
|
84 -force
|
|
|
85 #end if
|
|
|
86 #end if
|
|
|
87 </command>
|
|
|
88 <inputs>
|
|
|
89 <param name="param_in" type="data" format="featurexml,consensusxml,mzml,idxml" multiple="true" optional="True" size="30" label="Input files to transform (separated by blanks)" help="(-in) ">
|
|
|
90 <sanitizer>
|
|
|
91 <valid initial="string.printable">
|
|
|
92 <remove value="'"/>
|
|
|
93 <remove value="""/>
|
|
|
94 </valid>
|
|
|
95 </sanitizer>
|
|
|
96 </param>
|
|
|
97 <param name="param_trafo_in" type="data" format="trafoxml" multiple="true" optional="False" size="30" label="Transformations to apply (files separated by blanks)" help="(-trafo_in) ">
|
|
|
98 <sanitizer>
|
|
|
99 <valid initial="string.printable">
|
|
|
100 <remove value="'"/>
|
|
|
101 <remove value="""/>
|
|
|
102 </valid>
|
|
|
103 </sanitizer>
|
|
|
104 </param>
|
|
|
105 <param name="param_invert" type="boolean" truevalue="-invert" falsevalue="" checked="false" optional="True" label="Invert transformations (approximatively) before applying them" help="(-invert) "/>
|
|
|
106 <param name="param_model_type" type="select" optional="True" value="none" label="Type of model" help="(-type) ">
|
|
|
107 <option value="none">none</option>
|
|
|
108 <option value="linear">linear</option>
|
|
|
109 <option value="b_spline">b_spline</option>
|
|
|
110 <option value="interpolated">interpolated</option>
|
|
|
111 </param>
|
|
|
112 <param name="param_model_linear_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression" falsevalue="" checked="false" optional="True" label="Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
|
|
|
113 <param name="param_model_b_spline_wavelength" type="float" min="0.0" optional="True" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
|
|
|
114 <param name="param_model_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for B-spline fitting" help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
|
|
|
115 <param name="param_model_b_spline_extrapolate" type="select" optional="True" value="linear" label="Method to use for extrapolation beyond the original data range" help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
|
|
|
116 <option value="linear">linear</option>
|
|
|
117 <option value="b_spline">b_spline</option>
|
|
|
118 <option value="constant">constant</option>
|
|
|
119 <option value="global_linear">global_linear</option>
|
|
|
120 </param>
|
|
|
121 <param name="param_model_b_spline_boundary_condition" type="integer" min="0" max="2" optional="True" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help="(-boundary_condition) "/>
|
|
|
122 <param name="param_model_interpolated_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply" help="(-interpolation_type) ">
|
|
|
123 <option value="linear">linear</option>
|
|
|
124 <option value="cspline">cspline</option>
|
|
|
125 <option value="akima">akima</option>
|
|
|
126 </param>
|
|
|
127 <expand macro="advanced_options">
|
|
|
128 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
129 </expand>
|
|
|
130 </inputs>
|
|
|
131 <outputs>
|
|
|
132 <data name="param_out" metadata_source="param_in" format="input"/>
|
|
|
133 <data name="param_trafo_out" format="trafoxml"/>
|
|
|
134 </outputs>
|
|
|
135 <help>**What it does**
|
|
|
136
|
|
|
137 Applies retention time transformations to maps.
|
|
|
138
|
|
|
139
|
|
|
140 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html</help>
|
|
|
141 <expand macro="references"/>
|
|
|
142 </tool>
|
