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comparison RTModel.xml @ 3:4e9e33ca49c0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9
author galaxyp
date Fri, 14 Jul 2017 19:15:11 -0400
parents 5be3bb0724e9
children 9aa90b293884
comparison
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2:5cbd922478a7 3:4e9e33ca49c0
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: [Peptide property prediction]--> 3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <tool id="RTModel" name="RTModel" version="2.1.0"> 4 <tool id="RTModel" name="RTModel" version="2.2.0">
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 </macros> 9 </macros>
22 -in_negative $param_in_negative 22 -in_negative $param_in_negative
23 #end if 23 #end if
24 #if $param_out: 24 #if $param_out:
25 -out $param_out 25 -out $param_out
26 #end if 26 #end if
27 #if $param_out_oligo_params:
28 -out_oligo_params $param_out_oligo_params
29 #end if
30 #if $param_out_oligo_trainset:
31 -out_oligo_trainset $param_out_oligo_trainset
32 #end if
27 #if $param_svm_type: 33 #if $param_svm_type:
28 -svm_type 34 -svm_type
29 #if " " in str($param_svm_type): 35 #if " " in str($param_svm_type):
30 "$param_svm_type" 36 "$param_svm_type"
31 #else 37 #else
132 -force 138 -force
133 #end if 139 #end if
134 #end if 140 #end if
135 </command> 141 </command>
136 <inputs> 142 <inputs>
137 <param name="param_in" type="data" format="txt,idxml" 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;"/> 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;"/>
138 <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/> 144 <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/>
139 <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/> 145 <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/>
140 <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) "> 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) ">
141 <option value="NU_SVR" selected="true">NU_SVR</option> 147 <option value="NU_SVR" selected="true">NU_SVR</option>
142 <option value="NU_SVC">NU_SVC</option> 148 <option value="NU_SVC">NU_SVC</option>
182 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 188 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
183 </expand> 189 </expand>
184 </inputs> 190 </inputs>
185 <outputs> 191 <outputs>
186 <data name="param_out" format="txt"/> 192 <data name="param_out" format="txt"/>
193 <data name="param_out_oligo_params" format="paramXML"/>
194 <data name="param_out_oligo_trainset" format="txt"/>
187 </outputs> 195 </outputs>
188 <help>Trains a model for the retention time prediction of peptides from a training set. 196 <help>Trains a model for the retention time prediction of peptides from a training set.
189 197
190 198
191 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help> 199 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_RTModel.html</help>