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comparison PTModel.xml @ 12:f99faf6ad72f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:58:31 -0400
parents 8395234353a2
children 6f77453062f0
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11:c1697e1c0d50 12:f99faf6ad72f
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 CTDConverter.-->
3 <!--Proposed Tool Section: [Peptide property prediction]--> 3 <!--Proposed Tool Section: [Peptide property prediction]-->
4 <tool id="PTModel" name="PTModel" version="2.2.0"> 4 <tool id="PTModel" name="PTModel" version="2.3.0">
5 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description> 5 <description>Trains a model for the prediction of proteotypic peptides from a training set.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PTModel</token> 7 <token name="@EXECUTABLE@">PTModel</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>PTModel 13 <command detect_errors="aggressive"><![CDATA[PTModel
14 14
15 #if $param_in_positive: 15 #if $param_in_positive:
16 -in_positive $param_in_positive 16 -in_positive $param_in_positive
17 #end if 17 #end if
18 #if $param_in_negative: 18 #if $param_in_negative:
115 #if $adv_opts.adv_opts_selector=='advanced': 115 #if $adv_opts.adv_opts_selector=='advanced':
116 #if $adv_opts.param_force: 116 #if $adv_opts.param_force:
117 -force 117 -force
118 #end if 118 #end if
119 #end if 119 #end if
120 </command> 120 ]]></command>
121 <inputs> 121 <inputs>
122 <param name="param_in_positive" type="data" format="idxml" optional="False" label="input file with positive examples" help="(-in_positive) "/> 122 <param name="param_in_positive" type="data" format="idxml" optional="False" label="input file with positive examples" help="(-in_positive) "/>
123 <param name="param_in_negative" type="data" format="idxml" optional="False" label="input file with negative examples" help="(-in_negative) "/> 123 <param name="param_in_negative" type="data" format="idxml" optional="False" label="input file with negative examples" help="(-in_negative) "/>
124 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/> 124 <param name="param_c" type="float" value="1.0" label="the penalty parameter of the svm" help="(-c) "/>
125 <param name="param_svm_type" display="radio" type="select" optional="False" value="C_SVC" label="the type of the svm (NU_SVC or C_SVC)" help="(-svm_type) "> 125 <param name="param_svm_type" display="radio" type="select" optional="False" value="C_SVC" label="the type of the svm (NU_SVC or C_SVC)" help="(-svm_type) ">
164 <data name="param_out" format="txt"/> 164 <data name="param_out" format="txt"/>
165 </outputs> 165 </outputs>
166 <help>Trains a model for the prediction of proteotypic peptides from a training set. 166 <help>Trains a model for the prediction of proteotypic peptides from a training set.
167 167
168 168
169 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTModel.html</help> 169 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PTModel.html</help>
170 </tool> 170 </tool>