Mercurial > repos > galaxyp > openms_rtmodel
diff RTModel.xml @ 1:b68f859bd5f3 draft
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 |
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--- a/RTModel.xml Wed Mar 01 12:32:28 2017 -0500 +++ b/RTModel.xml Wed Aug 09 09:19:45 2017 -0400 @@ -1,7 +1,7 @@ <?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [Peptide property prediction]--> -<tool id="RTModel" name="RTModel" version="2.1.0"> +<tool id="RTModel" name="RTModel" version="2.2.0"> <description>Trains a model for the retention time prediction of peptides from a training set.</description> <macros> <token name="@EXECUTABLE@">RTModel</token> @@ -24,8 +24,19 @@ #if $param_out: -out $param_out #end if +#if $param_out_oligo_params: + -out_oligo_params $param_out_oligo_params +#end if +#if $param_out_oligo_trainset: + -out_oligo_trainset $param_out_oligo_trainset +#end if #if $param_svm_type: - -svm_type $param_svm_type + -svm_type + #if " " in str($param_svm_type): + "$param_svm_type" + #else + $param_svm_type + #end if #end if #if $param_nu: -nu $param_nu @@ -37,7 +48,12 @@ -c $param_c #end if #if $param_kernel_type: - -kernel_type $param_kernel_type + -kernel_type + #if " " in str($param_kernel_type): + "$param_kernel_type" + #else + $param_kernel_type + #end if #end if #if $param_degree: -degree $param_degree @@ -124,7 +140,7 @@ #end if </command> <inputs> - <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>"/> + <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>"/> <param name="param_in_positive" type="data" format="idxml" optional="True" label="input file with positive examples (peptide separation prediction)" help="(-in_positive) "/> <param name="param_in_negative" type="data" format="idxml" optional="True" label="input file with negative examples (peptide separation prediction)" help="(-in_negative) "/> <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) "> @@ -174,6 +190,8 @@ </inputs> <outputs> <data name="param_out" format="txt"/> + <data name="param_out_oligo_params" format="paramXML"/> + <data name="param_out_oligo_trainset" format="txt"/> </outputs> <help>Trains a model for the retention time prediction of peptides from a training set.