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comparison MapRTTransformer.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
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3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="MapRTTransformer" name="MapRTTransformer" version="1.12.0"> 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 <description>Applies retention time transformations to maps.</description> 3 <!--Proposed Tool Section: [Map Alignment]-->
4 <macros> 4 <tool id="MapRTTransformer" name="MapRTTransformer" version="2.0.0">
5 <token name="@EXECUTABLE@">MapRTTransformer</token> 5 <description>Applies retention time transformations to maps.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">MapRTTransformer</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>MapRTTransformer 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MapRTTransformer
11 14
12 -in ${param_in} 15 #if $param_in:
13 -out ${param_out} 16 -in $param_in
14 -trafo_in ${param_trafo_in} 17 #end if
15 -trafo_out ${param_trafo_out} 18 #if $param_out:
16 ${param_invert} 19 -out $param_out
17 -threads \${GALAXY_SLOTS:-24} 20 #end if
18 -model:type ${param_type} 21 #if $param_trafo_in:
19 ${param_symmetric_regression} 22 -trafo_in $param_trafo_in
20 -model:interpolated:interpolation_type ${param_interpolation_type} 23 #end if
24 #if $param_trafo_out:
25 -trafo_out $param_trafo_out
26 #end if
27 #if $param_invert:
28 -invert
29 #end if
30 #if $param_store_original_rt:
31 -store_original_rt
32 #end if
33 -threads \${GALAXY_SLOTS:-24}
34 #if $param_model_type:
35 -model:type
36 #if &quot; &quot; in str($param_model_type):
37 &quot;$param_model_type&quot;
38 #else
39 $param_model_type
40 #end if
41 #end if
42 #if $param_model_linear_symmetric_regression:
43 -model:linear:symmetric_regression
44 #end if
45 #if $param_model_b_spline_wavelength:
46 -model:b_spline:wavelength $param_model_b_spline_wavelength
47 #end if
48 #if $param_model_b_spline_num_nodes:
49 -model:b_spline:num_nodes $param_model_b_spline_num_nodes
50 #end if
51 #if $param_model_b_spline_extrapolate:
52 -model:b_spline:extrapolate
53 #if &quot; &quot; in str($param_model_b_spline_extrapolate):
54 &quot;$param_model_b_spline_extrapolate&quot;
55 #else
56 $param_model_b_spline_extrapolate
57 #end if
58 #end if
59 #if $param_model_b_spline_boundary_condition:
60 -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
61 #end if
62 #if $param_model_interpolated_interpolation_type:
63 -model:interpolated:interpolation_type
64 #if &quot; &quot; in str($param_model_interpolated_interpolation_type):
65 &quot;$param_model_interpolated_interpolation_type&quot;
66 #else
67 $param_model_interpolated_interpolation_type
68 #end if
69 #end if
70 #if $adv_opts.adv_opts_selector=='advanced':
71 #if $adv_opts.param_force:
72 -force
73 #end if
74 #end if
21 </command> 75 </command>
22 <inputs> 76 <inputs>
23 <param name="param_in" type="data" format="mzML,featureXML,consensusXML,idXML" optional="True" size="20" label="Input files to transform (separated by blanks)" help="(-in)"/> 77 <param format="xml,consensusxml,mzml" help="(-in) " label="Input file to transform (separated by blanks)" name="param_in" optional="True" type="data"/>
24 <param name="param_trafo_in" type="data" format="" optional="False" size="20" label="Transformations to apply (files separated by blanks)" help="(-trafo_in)"/> 78 <param format="trafoxml" help="(-trafo_in) " label="Transformation to apply" name="param_trafo_in" optional="False" type="data"/>
25 <param name="param_invert" type="boolean" truevalue="-invert true" falsevalue="-invert false" checked="false" optional="True" label="Invert transformations (approximatively) before applying them" help="(-invert)"/> 79 <param checked="false" falsevalue="" help="(-invert) " label="Invert transformation (approximatively) before applying it" name="param_invert" optional="True" truevalue="-invert" type="boolean"/>
26 <param name="param_type" type="select" optional="True" value="none" label="Type of model" help="(-type)"> 80 <param checked="false" falsevalue="" help="(-store_original_rt) " label="Store the original retention times (before transformation) as meta data in the output file" name="param_store_original_rt" optional="True" truevalue="-store_original_rt" type="boolean"/>
27 <option value="none">none</option> 81 <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="none">
28 <option value="linear">linear</option> 82 <option value="none">none</option>
29 <option value="b_spline">b_spline</option> 83 <option value="linear">linear</option>
30 <option value="interpolated">interpolated</option> 84 <option value="b_spline">b_spline</option>
31 </param> 85 <option value="interpolated">interpolated</option>
32 <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/> 86 </param>
33 <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)"> 87 <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Perform linear regression on 'y - x' vs" name="param_model_linear_symmetric_regression" optional="True" truevalue="-model:linear:symmetric_regression" type="boolean"/>
34 <option value="linear">linear</option> 88 <param 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" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" min="0.0" name="param_model_b_spline_wavelength" optional="True" type="float" value="0.0"/>
35 <option value="cspline">cspline</option> 89 <param help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing" label="Number of nodes for B-spline fitting" min="0" name="param_model_b_spline_num_nodes" optional="True" type="integer" value="5"/>
36 <option value="akima">akima</option> 90 <param 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)" label="Method to use for extrapolation beyond the original data range" name="param_model_b_spline_extrapolate" optional="True" type="select" value="linear">
37 </param> 91 <option value="linear">linear</option>
38 </inputs> 92 <option value="b_spline">b_spline</option>
39 <outputs> 93 <option value="constant">constant</option>
40 <data name="param_out" label="Output files separated by blanks. Either this option or 'trafo_out' have to be provided. They can be used together." format="idXML"> 94 <option value="global_linear">global_linear</option>
41 <change_format> 95 </param>
42 <when input="param_out_type" value="mzML" format="mzML"/> 96 <param help="(-boundary_condition) " label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" max="2" min="0" name="param_model_b_spline_boundary_condition" optional="True" type="integer" value="2"/>
43 <when input="param_out_type" value="featureXML" format="featureXML"/> 97 <param help="(-interpolation_type) " label="Type of interpolation to apply" name="param_model_interpolated_interpolation_type" optional="True" type="select" value="cspline">
44 <when input="param_out_type" value="consensusXML" format="consensusXML"/> 98 <option value="linear">linear</option>
45 </change_format> 99 <option value="cspline">cspline</option>
46 </data> 100 <option value="akima">akima</option>
47 <data name="param_trafo_out" label="Transformation output files separated by blanks. Either this option or 'out' have to be provided. They can be used together." format="data"/> 101 </param>
48 </outputs> 102 <expand macro="advanced_options">
49 <help>**What it does** 103 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
50 104 </expand>
51 Applies retention time transformations to maps. 105 </inputs>
106 <outputs>
107 <data format="input" metadata_source="param_in" name="param_out"/>
108 <data format="trafoxml" name="param_trafo_out"/>
109 </outputs>
110 <help>Applies retention time transformations to maps.
52 111
53 112
54 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html 113 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapRTTransformer.html</help>
55 114 </tool>
56 @REFERENCES@
57 </help>
58 </tool>