Mercurial > repos > galaxyp > openms_rtmodel
comparison RTModel.xml @ 1:b68f859bd5f3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 09 Aug 2017 09:19:45 -0400 |
parents | 8480765683cf |
children | c3da4387e137 |
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0:8480765683cf | 1:b68f859bd5f3 |
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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. <br>"/> | 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. <br>"/> |
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 <br>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 <br>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> |