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comparison RTModel.xml @ 8:a9ece00a3e54 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:07:56 +0000
parents 6d4530bc334c
children 654e2bf18e82
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7:6d4530bc334c 8:a9ece00a3e54
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 CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Peptide property prediction]--> 3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <tool id="RTModel" name="RTModel" version="2.3.0"> 4 <tool id="RTModel" name="RTModel" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Trains a model for the retention time prediction of peptides from a training set.</description> 5 <description>Trains a model for the retention time prediction of peptides from a training set.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RTModel</token> 7 <token name="@EXECUTABLE@">RTModel</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[RTModel 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 #if $in:
20 mkdir in &&
21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
17 #end if 22 #end if
18 #if $param_in_positive: 23 #if $in_positive:
19 -in_positive $param_in_positive 24 mkdir in_positive &&
25 ln -s '$in_positive' 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)' &&
20 #end if 26 #end if
21 #if $param_in_negative: 27 #if $in_negative:
22 -in_negative $param_in_negative 28 mkdir in_negative &&
29 ln -s '$in_negative' 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)' &&
23 #end if 30 #end if
24 #if $param_out: 31 mkdir out &&
25 -out $param_out 32 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
33 mkdir out_oligo_params &&
26 #end if 34 #end if
27 #if $param_out_oligo_params: 35 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 -out_oligo_params $param_out_oligo_params 36 mkdir out_oligo_trainset &&
29 #end if 37 #end if
30 #if $param_out_oligo_trainset: 38
31 -out_oligo_trainset $param_out_oligo_trainset 39 ## Main program call
40
41 set -o pipefail &&
42 @EXECUTABLE@ -write_ctd ./ &&
43 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
44 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
45 #if $in:
46 -in
47 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
32 #end if 48 #end if
33 #if $param_svm_type: 49 #if $in_positive:
34 -svm_type 50 -in_positive
35 #if " " in str($param_svm_type): 51 'in_positive/${re.sub("[^\w\-_]", "_", $in_positive.element_identifier)}.$gxy2omsext($in_positive.ext)'
36 "$param_svm_type"
37 #else
38 $param_svm_type
39 #end if
40 #end if 52 #end if
41 #if $param_nu: 53 #if $in_negative:
42 -nu $param_nu 54 -in_negative
55 'in_negative/${re.sub("[^\w\-_]", "_", $in_negative.element_identifier)}.$gxy2omsext($in_negative.ext)'
43 #end if 56 #end if
44 #if $param_p: 57 -out
45 -p $param_p 58 'out/output.${gxy2omsext("txt")}'
59 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
60 -out_oligo_params
61 'out_oligo_params/output.${gxy2omsext("paramxml")}'
46 #end if 62 #end if
47 #if $param_c: 63 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
48 -c $param_c 64 -out_oligo_trainset
65 'out_oligo_trainset/output.${gxy2omsext("txt")}'
49 #end if 66 #end if
50 #if $param_kernel_type: 67 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
51 -kernel_type 68 | tee '$stdout'
52 #if " " in str($param_kernel_type):
53 "$param_kernel_type"
54 #else
55 $param_kernel_type
56 #end if
57 #end if 69 #end if
58 #if $param_degree: 70
59 -degree $param_degree 71 ## Postprocessing
72 && mv 'out/output.${gxy2omsext("txt")}' '$out'
73 #if "out_oligo_params_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
74 && mv 'out_oligo_params/output.${gxy2omsext("paramxml")}' '$out_oligo_params'
60 #end if 75 #end if
61 #if $param_border_length: 76 #if "out_oligo_trainset_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
62 -border_length $param_border_length 77 && mv 'out_oligo_trainset/output.${gxy2omsext("txt")}' '$out_oligo_trainset'
63 #end if 78 #end if
64 #if $param_max_std: 79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
65 -max_std $param_max_std 80 && mv '@EXECUTABLE@.ctd' '$ctd_out'
66 #end if 81 #end if]]></command>
67 #if $param_k_mer_length: 82 <configfiles>
68 -k_mer_length $param_k_mer_length 83 <inputs name="args_json" data_style="paths"/>
69 #end if 84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
70 #if $param_sigma: 85 </configfiles>
71 -sigma $param_sigma
72 #end if
73 #if $param_total_gradient_time:
74 -total_gradient_time $param_total_gradient_time
75 #end if
76 #if $param_first_dim_rt:
77 -first_dim_rt
78 #end if
79 #if $param_additive_cv:
80 -additive_cv
81 #end if
82 #if $param_cv_skip_cv:
83 -cv:skip_cv
84 #end if
85 #if $param_cv_number_of_runs:
86 -cv:number_of_runs $param_cv_number_of_runs
87 #end if
88 #if $param_cv_number_of_partitions:
89 -cv:number_of_partitions $param_cv_number_of_partitions
90 #end if
91 #if $param_cv_degree_start:
92 -cv:degree_start $param_cv_degree_start
93 #end if
94 #if $param_cv_degree_step_size:
95 -cv:degree_step_size $param_cv_degree_step_size
96 #end if
97 #if $param_cv_degree_stop:
98 -cv:degree_stop $param_cv_degree_stop
99 #end if
100 #if $param_cv_p_start:
101 -cv:p_start $param_cv_p_start
102 #end if
103 #if $param_cv_p_step_size:
104 -cv:p_step_size $param_cv_p_step_size
105 #end if
106 #if $param_cv_p_stop:
107 -cv:p_stop $param_cv_p_stop
108 #end if
109 #if $param_cv_c_start:
110 -cv:c_start $param_cv_c_start
111 #end if
112 #if $param_cv_c_step_size:
113 -cv:c_step_size $param_cv_c_step_size
114 #end if
115 #if $param_cv_c_stop:
116 -cv:c_stop $param_cv_c_stop
117 #end if
118 #if $param_cv_nu_start:
119 -cv:nu_start $param_cv_nu_start
120 #end if
121 #if $param_cv_nu_step_size:
122 -cv:nu_step_size $param_cv_nu_step_size
123 #end if
124 #if $param_cv_nu_stop:
125 -cv:nu_stop $param_cv_nu_stop
126 #end if
127 #if $param_cv_sigma_start:
128 -cv:sigma_start $param_cv_sigma_start
129 #end if
130 #if $param_cv_sigma_step_size:
131 -cv:sigma_step_size $param_cv_sigma_step_size
132 #end if
133 #if $param_cv_sigma_stop:
134 -cv:sigma_stop $param_cv_sigma_stop
135 #end if
136 #if $adv_opts.adv_opts_selector=='advanced':
137 #if $adv_opts.param_force:
138 -force
139 #end if
140 #end if
141 ]]></command>
142 <inputs> 86 <inputs>
143 <param name="param_in" type="data" format="idxml,txt" optional="True" label="This is the name of the input file (RT prediction)" help="(-in) It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line. &lt;br&gt;"/> 87 <param name="in" argument="-in" type="data" format="idxml,txt" optional="true" label="This is the name of the input file (RT prediction)" help="It is assumed that the file type is idXML. Alternatively you can provide a .txt file having a sequence and the corresponding rt per line.. select idxml,txt data sets(s)"/>
144 <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/> 88 <param name="in_positive" argument="-in_positive" type="data" format="idxml" optional="true" label="input file with positive examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
145 <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/> 89 <param name="in_negative" argument="-in_negative" type="data" format="idxml" optional="true" label="input file with negative examples (peptide separation prediction)" help=" select idxml data sets(s)"/>
146 <param name="param_svm_type" display="radio" type="select" optional="False" value="NU_SVR" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set &lt;br&gt;to C_SVC for separation prediction)" help="(-svm_type) "> 90 <param name="svm_type" argument="-svm_type" display="radio" type="select" optional="false" label="the type of the svm (NU_SVR or EPSILON_SVR for RT prediction, automatically set" help="to C_SVC for separation prediction). ">
147 <option value="NU_SVR" selected="true">NU_SVR</option> 91 <option value="NU_SVR" selected="true">NU_SVR</option>
148 <option value="NU_SVC">NU_SVC</option> 92 <option value="NU_SVC">NU_SVC</option>
149 <option value="EPSILON_SVR">EPSILON_SVR</option> 93 <option value="EPSILON_SVR">EPSILON_SVR</option>
150 <option value="C_SVC">C_SVC</option> 94 <option value="C_SVC">C_SVC</option>
95 <expand macro="list_string_san"/>
151 </param> 96 </param>
152 <param name="param_nu" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help="(-nu) "/> 97 <param name="nu" argument="-nu" type="float" optional="true" min="0.0" max="1.0" value="0.5" label="the nu parameter [0..1] of the svm (for nu-SVR)" help=""/>
153 <param name="param_p" type="float" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help="(-p) "/> 98 <param name="p" argument="-p" type="float" optional="true" value="0.1" label="the epsilon parameter of the svm (for epsilon-SVR)" help=""/>
154 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/> 99 <param name="c" argument="-c" type="float" optional="true" value="1.0" label="the penalty parameter of the svm" help=""/>
155 <param name="param_kernel_type" display="radio" type="select" optional="False" value="OLIGO" label="the kernel type of the svm" help="(-kernel_type) "> 100 <param name="kernel_type" argument="-kernel_type" display="radio" type="select" optional="false" label="the kernel type of the svm" help="">
156 <option value="LINEAR">LINEAR</option> 101 <option value="LINEAR">LINEAR</option>
157 <option value="RBF">RBF</option> 102 <option value="RBF">RBF</option>
158 <option value="POLY">POLY</option> 103 <option value="POLY">POLY</option>
159 <option value="OLIGO" selected="true">OLIGO</option> 104 <option value="OLIGO" selected="true">OLIGO</option>
105 <expand macro="list_string_san"/>
160 </param> 106 </param>
161 <param name="param_degree" type="integer" min="1" optional="True" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help="(-degree) "/> 107 <param name="degree" argument="-degree" type="integer" optional="true" min="1" value="1" label="the degree parameter of the kernel function of the svm (POLY kernel)" help=""/>
162 <param name="param_border_length" type="integer" min="1" optional="True" value="22" label="length of the POBK" help="(-border_length) "/> 108 <param name="border_length" argument="-border_length" type="integer" optional="true" min="1" value="22" label="length of the POBK" help=""/>
163 <param name="param_max_std" type="float" min="0.0" optional="True" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help="(-max_std) "/> 109 <param name="max_std" argument="-max_std" type="float" optional="true" min="0.0" value="10.0" label="max standard deviation for a peptide to be included (if there are several ones for one peptide string)(median is taken)" help=""/>
164 <param name="param_k_mer_length" type="integer" min="1" optional="True" value="1" label="k_mer length of the POBK" help="(-k_mer_length) "/> 110 <param name="k_mer_length" argument="-k_mer_length" type="integer" optional="true" min="1" value="1" label="k_mer length of the POBK" help=""/>
165 <param name="param_sigma" type="float" value="5.0" label="sigma of the POBK" help="(-sigma) "/> 111 <param name="sigma" argument="-sigma" type="float" optional="true" value="5.0" label="sigma of the POBK" help=""/>
166 <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help="(-total_gradient_time) "/> 112 <param name="total_gradient_time" argument="-total_gradient_time" type="float" optional="true" min="1e-05" value="1.0" label="the time (in seconds) of the gradient (only for RT prediction)" help=""/>
167 <param name="param_first_dim_rt" display="radio" type="boolean" truevalue="-first_dim_rt" falsevalue="" checked="false" optional="True" label="if set the model will be built for first_dim_rt" help="(-first_dim_rt) "/> 113 <param name="first_dim_rt" argument="-first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if set the model will be built for first_dim_rt" help=""/>
168 <param name="param_additive_cv" display="radio" type="boolean" truevalue="-additive_cv" falsevalue="" checked="false" optional="True" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied &lt;br&gt;with the step size to get the new value" help="(-additive_cv) "/> 114 <param name="additive_cv" argument="-additive_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if the step sizes should be interpreted additively (otherwise the actual value is multiplied" help="with the step size to get the new value"/>
169 <param name="param_cv_skip_cv" display="radio" type="boolean" truevalue="-cv:skip_cv" falsevalue="" checked="false" optional="True" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help="(-skip_cv) "/> 115 <section name="cv" title="Parameters for the grid search / cross validation:" help="" expanded="false">
170 <param name="param_cv_number_of_runs" type="integer" min="1" optional="True" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help="(-number_of_runs) "/> 116 <param name="skip_cv" argument="-cv:skip_cv" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set to enable Cross-Validation or set to true if the model should just be trained with 1 set of specified parameters" help=""/>
171 <param name="param_cv_number_of_partitions" type="integer" min="2" optional="True" value="10" label="number of CV partitions" help="(-number_of_partitions) "/> 117 <param name="number_of_runs" argument="-cv:number_of_runs" type="integer" optional="true" min="1" value="1" label="number of runs for the CV (each run creates a new random partition of the data)" help=""/>
172 <param name="param_cv_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start) "/> 118 <param name="number_of_partitions" argument="-cv:number_of_partitions" type="integer" optional="true" min="2" value="10" label="number of CV partitions" help=""/>
173 <param name="param_cv_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size) "/> 119 <param name="degree_start" argument="-cv:degree_start" type="integer" optional="true" min="1" value="1" label="starting point of degree" help=""/>
174 <param name="param_cv_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop) "/> 120 <param name="degree_step_size" argument="-cv:degree_step_size" type="integer" optional="true" value="2" label="step size point of degree" help=""/>
175 <param name="param_cv_p_start" type="float" value="1.0" label="starting point of p" help="(-p_start) "/> 121 <param name="degree_stop" argument="-cv:degree_stop" type="integer" optional="true" value="4" label="stopping point of degree" help=""/>
176 <param name="param_cv_p_step_size" type="float" value="10.0" label="step size point of p" help="(-p_step_size) "/> 122 <param name="p_start" argument="-cv:p_start" type="float" optional="true" value="1.0" label="starting point of p" help=""/>
177 <param name="param_cv_p_stop" type="float" value="1000.0" label="stopping point of p" help="(-p_stop) "/> 123 <param name="p_step_size" argument="-cv:p_step_size" type="float" optional="true" value="10.0" label="step size point of p" help=""/>
178 <param name="param_cv_c_start" type="float" value="1.0" label="starting point of c" help="(-c_start) "/> 124 <param name="p_stop" argument="-cv:p_stop" type="float" optional="true" value="1000.0" label="stopping point of p" help=""/>
179 <param name="param_cv_c_step_size" type="float" value="10.0" label="step size of c" help="(-c_step_size) "/> 125 <param name="c_start" argument="-cv:c_start" type="float" optional="true" value="1.0" label="starting point of c" help=""/>
180 <param name="param_cv_c_stop" type="float" value="1000.0" label="stopping point of c" help="(-c_stop) "/> 126 <param name="c_step_size" argument="-cv:c_step_size" type="float" optional="true" value="10.0" label="step size of c" help=""/>
181 <param name="param_cv_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start) "/> 127 <param name="c_stop" argument="-cv:c_stop" type="float" optional="true" value="1000.0" label="stopping point of c" help=""/>
182 <param name="param_cv_nu_step_size" type="float" value="1.2" label="step size of nu" help="(-nu_step_size) "/> 128 <param name="nu_start" argument="-cv:nu_start" type="float" optional="true" min="0.0" max="1.0" value="0.3" label="starting point of nu" help=""/>
183 <param name="param_cv_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="stopping point of nu" help="(-nu_stop) "/> 129 <param name="nu_step_size" argument="-cv:nu_step_size" type="float" optional="true" value="1.2" label="step size of nu" help=""/>
184 <param name="param_cv_sigma_start" type="float" value="1.0" label="starting point of sigma" help="(-sigma_start) "/> 130 <param name="nu_stop" argument="-cv:nu_stop" type="float" optional="true" min="0.0" max="1.0" value="0.7" label="stopping point of nu" help=""/>
185 <param name="param_cv_sigma_step_size" type="float" value="1.3" label="step size of sigma" help="(-sigma_step_size) "/> 131 <param name="sigma_start" argument="-cv:sigma_start" type="float" optional="true" value="1.0" label="starting point of sigma" help=""/>
186 <param name="param_cv_sigma_stop" type="float" value="15.0" label="stopping point of sigma" help="(-sigma_stop) "/> 132 <param name="sigma_step_size" argument="-cv:sigma_step_size" type="float" optional="true" value="1.3" label="step size of sigma" help=""/>
187 <expand macro="advanced_options"> 133 <param name="sigma_stop" argument="-cv:sigma_stop" type="float" optional="true" value="15.0" label="stopping point of sigma" help=""/>
188 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 134 </section>
135 <expand macro="adv_opts_macro">
136 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
137 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
138 <expand macro="list_string_san"/>
139 </param>
189 </expand> 140 </expand>
141 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
142 <option value="out_oligo_params_FLAG">out_oligo_params (stopping point of sigma)</option>
143 <option value="out_oligo_trainset_FLAG">out_oligo_trainset (stopping point of sigma)</option>
144 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
145 </param>
190 </inputs> 146 </inputs>
191 <outputs> 147 <outputs>
192 <data name="param_out" format="txt"/> 148 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
193 <data name="param_out_oligo_params" format="paramXML"/> 149 <data name="out_oligo_params" label="${tool.name} on ${on_string}: out_oligo_params" format="paramxml">
194 <data name="param_out_oligo_trainset" format="txt"/> 150 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_params_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data>
152 <data name="out_oligo_trainset" label="${tool.name} on ${on_string}: out_oligo_trainset" format="txt">
153 <filter>OPTIONAL_OUTPUTS is not None and "out_oligo_trainset_FLAG" in OPTIONAL_OUTPUTS</filter>
154 </data>
155 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
156 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
157 </data>
195 </outputs> 158 </outputs>
196 <help>Trains a model for the retention time prediction of peptides from a training set. 159 <tests>
160 <expand macro="autotest_RTModel"/>
161 <expand macro="manutest_RTModel"/>
162 </tests>
163 <help><![CDATA[Trains a model for the retention time prediction of peptides from a training set.
197 164
198 165
199 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_RTModel.html</help> 166 For more information, visit http://www.openms.de/documentation/TOPP_RTModel.html]]></help>
167 <expand macro="references"/>
200 </tool> 168 </tool>