view SvmTheoreticalSpectrumGeneratorTrainer.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="1.12.0">
  <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description>
  <macros>
    <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SvmTheoreticalSpectrumGeneratorTrainer

-in_spectra ${param_in_spectra}
-in_identifications ${param_in_identifications}
-model_output_file ${param_model_output_file}
-precursor_charge ${param_precursor_charge}
${param_write_training_files}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:number_intensity_levels ${param_number_intensity_levels}
-algorithm:number_regions ${param_number_regions}
-algorithm:parent_tolerance ${param_parent_tolerance}
-algorithm:peak_tolerance ${param_peak_tolerance}
${param_add_b_ions}
${param_add_y_ions}
${param_add_a_ions}
${param_add_c_ions}
${param_add_x_ions}
${param_add_z_ions}
${param_add_losses}
${param_add_b2_ions}
${param_add_y2_ions}
-algorithm:svm:svc_type ${param_svc_type}
-algorithm:svm:svr_type ${param_svr_type}
${param_scaling}
-algorithm:svm:scaling_lower ${param_scaling_lower}
-algorithm:svm:scaling_upper ${param_scaling_upper}
-algorithm:svm:n_fold ${param_n_fold}
${param_grid}
${param_additive_cv}
-algorithm:svm:svc:kernel_type ${param_kernel_type}
-algorithm:svm:svc:degree ${param_degree}
-algorithm:svm:svc:gamma ${param_gamma}
-algorithm:svm:svc:C ${param_C}
-algorithm:svm:svc:nu ${param_nu}
${param_balancing}
-algorithm:svm:svc:degree_start ${param_degree_start}
-algorithm:svm:svc:degree_step_size ${param_degree_step_size}
-algorithm:svm:svc:degree_stop ${param_degree_stop}
-algorithm:svm:svc:gamma_start ${param_gamma_start}
-algorithm:svm:svc:gamma_step_size ${param_gamma_step_size}
-algorithm:svm:svc:gamma_stop ${param_gamma_stop}
-algorithm:svm:svc:c_start ${param_c_start}
-algorithm:svm:svc:c_step_size ${param_c_step_size}
-algorithm:svm:svc:c_stop ${param_c_stop}
-algorithm:svm:svc:nu_start ${param_nu_start}
-algorithm:svm:svc:nu_step_size ${param_nu_step_size}
-algorithm:svm:svc:nu_stop ${param_nu_stop}
-algorithm:svm:svr:kernel_type ${param_kernel_type}
-algorithm:svm:svr:degree ${param_degree}
-algorithm:svm:svr:gamma ${param_gamma}
-algorithm:svm:svr:C ${param_C}
-algorithm:svm:svr:p ${param_p}
-algorithm:svm:svr:nu ${param_nu}
-algorithm:svm:svr:degree_start ${param_degree_start}
-algorithm:svm:svr:degree_step_size ${param_degree_step_size}
-algorithm:svm:svr:degree_stop ${param_degree_stop}
-algorithm:svm:svr:gamma_start ${param_gamma_start}
-algorithm:svm:svr:gamma_step_size ${param_gamma_step_size}
-algorithm:svm:svr:gamma_stop ${param_gamma_stop}
-algorithm:svm:svr:p_start ${param_p_start}
-algorithm:svm:svr:p_step_size ${param_p_step_size}
-algorithm:svm:svr:p_stop ${param_p_stop}
-algorithm:svm:svr:c_start ${param_c_start}
-algorithm:svm:svr:c_step_size ${param_c_step_size}
-algorithm:svm:svr:c_stop ${param_c_stop}
-algorithm:svm:svr:nu_start ${param_nu_start}
-algorithm:svm:svr:nu_step_size ${param_nu_step_size}
-algorithm:svm:svr:nu_stop ${param_nu_stop}
</command>
  <inputs>
    <param name="param_in_spectra" type="data" format="mzML" optional="False" label="Input Training Spectra in mzML" help="(-in_spectra)"/>
    <param name="param_in_identifications" type="data" format="idXML" optional="False" label="Input file with corresponding sequences in idXML" help="(-in_identifications)"/>
    <param name="param_precursor_charge" type="integer" min="1" max="3" optional="True" value="2" label="Precursor charge state used for model training" help="(-precursor_charge)"/>
    <param name="param_write_training_files" type="boolean" truevalue="-write_training_files true" falsevalue="-write_training_files false" checked="false" optional="True" label="No models are trained but input training files for libSVM command line tools are produced" help="(-write_training_files)"/>
    <param name="param_number_intensity_levels" type="integer" value="7" label="The number of intensity bins (for secondary type models)" help="(-number_intensity_levels)"/>
    <param name="param_number_regions" type="integer" value="3" label="The number of regions each spectrum is split to (for secondary type models)" help="(-number_regions)"/>
    <param name="param_parent_tolerance" type="float" value="2.5" label="The maximum difference between theoretical and experimental parent mass to accept training spectrum" help="(-parent_tolerance)"/>
    <param name="param_peak_tolerance" type="float" value="0.5" label="The maximum mass error for a peak to the expected mass of some ion type" help="(-peak_tolerance)"/>
    <param name="param_add_b_ions" type="boolean" truevalue="-algorithm:add_b_ions true" falsevalue="-algorithm:add_b_ions false" checked="true" optional="True" label="Train simulator for b-ions" help="(-add_b_ions)"/>
    <param name="param_add_y_ions" type="boolean" truevalue="-algorithm:add_y_ions true" falsevalue="-algorithm:add_y_ions false" checked="true" optional="True" label="Train simulator for y-ions" help="(-add_y_ions)"/>
    <param name="param_add_a_ions" type="boolean" truevalue="-algorithm:add_a_ions true" falsevalue="-algorithm:add_a_ions false" checked="false" optional="True" label="Train simulator for a-ions" help="(-add_a_ions)"/>
    <param name="param_add_c_ions" type="boolean" truevalue="-algorithm:add_c_ions true" falsevalue="-algorithm:add_c_ions false" checked="false" optional="True" label="Train simulator for c-ions" help="(-add_c_ions)"/>
    <param name="param_add_x_ions" type="boolean" truevalue="-algorithm:add_x_ions true" falsevalue="-algorithm:add_x_ions false" checked="false" optional="True" label="Train simulator for x-ions" help="(-add_x_ions)"/>
    <param name="param_add_z_ions" type="boolean" truevalue="-algorithm:add_z_ions true" falsevalue="-algorithm:add_z_ions false" checked="false" optional="True" label="Train simulator for z-ions" help="(-add_z_ions)"/>
    <param name="param_add_losses" type="boolean" truevalue="-algorithm:add_losses true" falsevalue="-algorithm:add_losses false" checked="false" optional="True" label="Train simulator for neutral losses of H2O and NH3 for b-ions and y-ions" help="(-add_losses)"/>
    <param name="param_add_b2_ions" type="boolean" truevalue="-algorithm:add_b2_ions true" falsevalue="-algorithm:add_b2_ions false" checked="false" optional="True" label="Train simulator for doubly charged b-ions" help="(-add_b2_ions)"/>
    <param name="param_add_y2_ions" type="boolean" truevalue="-algorithm:add_y2_ions true" falsevalue="-algorithm:add_y2_ions false" checked="false" optional="True" label="Train simulator for double charged y-ions" help="(-add_y2_ions)"/>
    <param name="param_svc_type" type="integer" min="0" max="1" optional="True" value="0" label="Type of the SVC: 0=C_SVC 1=NU_SVC" help="(-svc_type)"/>
    <param name="param_svr_type" type="integer" min="0" max="1" optional="True" value="1" label="Type of the SVR: 0=EPSILON_SVR 1=NU_SVR" help="(-svr_type)"/>
    <param name="param_scaling" type="boolean" truevalue="-algorithm:svm:scaling true" falsevalue="-algorithm:svm:scaling false" checked="true" optional="True" label="Apply scaling of feature values" help="(-scaling)"/>
    <param name="param_scaling_lower" type="float" value="0.0" label="Lower bound for scaling" help="(-scaling_lower)"/>
    <param name="param_scaling_upper" type="float" value="1.0" label="Upper bound for scaling" help="(-scaling_upper)"/>
    <param name="param_n_fold" type="integer" min="1" optional="True" value="5" label="n_fold cross validation is performed" help="(-n_fold)"/>
    <param name="param_grid" type="boolean" truevalue="-algorithm:svm:grid true" falsevalue="-algorithm:svm:grid false" checked="false" optional="True" label="Perform grid search" help="(-grid)"/>
    <param name="param_additive_cv" type="boolean" truevalue="-algorithm:svm:additive_cv true" falsevalue="-algorithm:svm:additive_cv false" checked="false" optional="True" label="Additive step size (if false multiplicative)" help="(-additive_cv)"/>
    <param name="param_kernel_type" type="integer" min="0" max="3" optional="True" value="2" label="Type of the kernel:  0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help="(-kernel_type)"/>
    <param name="param_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree)"/>
    <param name="param_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma)"/>
    <param name="param_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C)"/>
    <param name="param_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu)"/>
    <param name="param_balancing" type="boolean" truevalue="-algorithm:svm:svc:balancing true" falsevalue="-algorithm:svm:svc:balancing false" checked="true" optional="True" label="Use class balanced SVC training" help="(-balancing)"/>
    <param name="param_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start)"/>
    <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/>
    <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/>
    <param name="param_gamma_start" type="float" min="0.0" max="1.0" optional="True" value="1e-05" label="starting point of gamma" help="(-gamma_start)"/>
    <param name="param_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size)"/>
    <param name="param_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop)"/>
    <param name="param_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start)"/>
    <param name="param_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size)"/>
    <param name="param_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop)"/>
    <param name="param_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start)"/>
    <param name="param_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size)"/>
    <param name="param_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.6" label="stopping point of nu" help="(-nu_stop)"/>
    <param name="param_kernel_type" type="integer" min="0" max="3" optional="True" value="2" label="Type of the kernel:  0=LINEAR 1=POLY 2=RBF 3=SIGMOID" help="(-kernel_type)"/>
    <param name="param_degree" type="integer" min="1" optional="True" value="3" label="For POLY" help="(-degree)"/>
    <param name="param_gamma" type="float" min="0.0" optional="True" value="0.0" label="For POLY/RBF/SIGMOID" help="(-gamma)"/>
    <param name="param_C" type="float" value="1.0" label="Cost of constraint violation" help="(-C)"/>
    <param name="param_p" type="float" value="0.1" label="The epsilon for the loss function in epsilon-SVR" help="(-p)"/>
    <param name="param_nu" type="float" value="0.5" label="For NU_SVC, ONE_CLASS and NU_SVR" help="(-nu)"/>
    <param name="param_degree_start" type="integer" min="1" optional="True" value="1" label="starting point of degree" help="(-degree_start)"/>
    <param name="param_degree_step_size" type="integer" value="2" label="step size point of degree" help="(-degree_step_size)"/>
    <param name="param_degree_stop" type="integer" value="4" label="stopping point of degree" help="(-degree_stop)"/>
    <param name="param_gamma_start" type="float" min="0.0" max="1.0" optional="True" value="1e-05" label="starting point of gamma" help="(-gamma_start)"/>
    <param name="param_gamma_step_size" type="integer" value="100" label="step size point of gamma" help="(-gamma_step_size)"/>
    <param name="param_gamma_stop" type="float" value="0.1" label="stopping point of gamma" help="(-gamma_stop)"/>
    <param name="param_p_start" type="float" value="1e-05" label="starting point of p" help="(-p_start)"/>
    <param name="param_p_step_size" type="integer" value="100" label="step size point of p" help="(-p_step_size)"/>
    <param name="param_p_stop" type="float" value="0.1" label="stopping point of p" help="(-p_stop)"/>
    <param name="param_c_start" type="float" value="0.1" label="starting point of c" help="(-c_start)"/>
    <param name="param_c_step_size" type="integer" value="100" label="step size of c" help="(-c_step_size)"/>
    <param name="param_c_stop" type="integer" value="1000" label="stopping point of c" help="(-c_stop)"/>
    <param name="param_nu_start" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="starting point of nu" help="(-nu_start)"/>
    <param name="param_nu_step_size" type="integer" value="2" label="step size of nu" help="(-nu_step_size)"/>
    <param name="param_nu_stop" type="float" min="0.0" max="1.0" optional="True" value="0.6" label="stopping point of nu" help="(-nu_stop)"/>
  </inputs>
  <outputs>
    <data name="param_model_output_file" label="Name for output files. For each ion_type one file &lt;filename&gt;_residue_loss_charge.svm and one &lt;filename&gt;.info which has to be passed to the SvmTheoretical SpectrumGenerator" format="data"/>
  </outputs>
  <help>**What it does**

Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html

@REFERENCES@
</help>
</tool>