view RTPredict.xml @ 3:ec62782f6c68 draft

Uploaded

<?xml version='1.0' encoding='UTF-8'?>
<tool id="RTPredict" name="RTPredict" version="1.12.0">
  <description>Predicts retention times for peptides using a model trained by RTModel.</description>
  <macros>
    <token name="@EXECUTABLE@">RTPredict</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>RTPredict

-in_id ${param_in_id}
-in_text ${param_in_text}
-svm_model ${param_svm_model}
-total_gradient_time ${param_total_gradient_time}
-threads \${GALAXY_SLOTS:-24} 
-out_id:file ${param_file}
-out_id:positive ${param_positive}
-out_id:negative ${param_negative}
-out_text:file ${param_file}
#if $adv_opts.adv_opts_selector=='advanced':
    -max_number_of_peptides ${adv_opts.param_max_number_of_peptides}
    ${adv_opts.param_rewrite_peptideidentification_rtmz}
#end if
</command>
  <inputs>
    <param name="param_in_id" type="data" format="idXML" optional="True" label="Peptides with precursor information" help="(-in_id)"/>
    <param name="param_in_text" type="data" format="txt" optional="True" label="Peptides as text-based file" help="(-in_text)"/>
    <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by RTModel)" help="(-svm_model)"/>
    <param name="param_total_gradient_time" type="float" min="1e-05" optional="True" value="1.0" label="The time (in seconds) of the gradient (peptide RT prediction)" help="(-total_gradient_time)"/>
    <expand macro="advanced_options">
      <param name="param_max_number_of_peptides" type="integer" value="100000" label="The maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)." help="(-max_number_of_peptides)"/>
      <param name="param_rewrite_peptideidentification_rtmz" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz true" falsevalue="-out_id:rewrite_peptideidentification_rtmz false" checked="false" optional="True" label="Rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)" help="(-rewrite_peptideidentification_rtmz)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_file" label="Output file with peptide RT prediction" format="idXML"/>
    <data name="param_positive" label="Output file in idXML format containing positive predictions for peptide separation prediction - requires 'out_id:negative' to be present as well." format="idXML"/>
    <data name="param_negative" label="Output file in idXML format containing negative predictions for peptide separation prediction - requires 'out_id:positive' to be present as well." format="idXML"/>
    <data name="param_file" label="Output file with predicted RT values" format="tabular"/>
  </outputs>
  <help>**What it does**

Predicts retention times for peptides using a model trained by RTModel.


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

@REFERENCES@
</help>
</tool>