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comparison RTModel.xml @ 1:b68f859bd5f3 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 09:19:45 -0400
parents 8480765683cf
children c3da4387e137
comparison
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0:8480765683cf 1:b68f859bd5f3
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 $param_svm_type 34 -svm_type
35 #if " " in str($param_svm_type):
36 "$param_svm_type"
37 #else
38 $param_svm_type
39 #end if
29 #end if 40 #end if
30 #if $param_nu: 41 #if $param_nu:
31 -nu $param_nu 42 -nu $param_nu
32 #end if 43 #end if
33 #if $param_p: 44 #if $param_p:
35 #end if 46 #end if
36 #if $param_c: 47 #if $param_c:
37 -c $param_c 48 -c $param_c
38 #end if 49 #end if
39 #if $param_kernel_type: 50 #if $param_kernel_type:
40 -kernel_type $param_kernel_type 51 -kernel_type
52 #if " " in str($param_kernel_type):
53 "$param_kernel_type"
54 #else
55 $param_kernel_type
56 #end if
41 #end if 57 #end if
42 #if $param_degree: 58 #if $param_degree:
43 -degree $param_degree 59 -degree $param_degree
44 #end if 60 #end if
45 #if $param_border_length: 61 #if $param_border_length:
122 -force 138 -force
123 #end if 139 #end if
124 #end if 140 #end if
125 </command> 141 </command>
126 <inputs> 142 <inputs>
127 <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;"/>
128 <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) "/>
129 <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) "/>
130 <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) ">
131 <option value="NU_SVR" selected="true">NU_SVR</option> 147 <option value="NU_SVR" selected="true">NU_SVR</option>
132 <option value="NU_SVC">NU_SVC</option> 148 <option value="NU_SVC">NU_SVC</option>
172 <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) "/>
173 </expand> 189 </expand>
174 </inputs> 190 </inputs>
175 <outputs> 191 <outputs>
176 <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"/>
177 </outputs> 195 </outputs>
178 <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.
179 197
180 198
181 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>