comparison PTPredict.xml @ 0:3070d71e0e5c draft

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0:3070d71e0e5c

<?xml version='1.0' encoding='UTF-8'?>
<tool id="PTPredict" name="PTPredict" version="2.0.0">
  <description>predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel</description>
  <macros>
    <token name="@EXECUTABLE@">PTPredict</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PTPredict

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_svm_model:
  -svm_model $param_svm_model
#end if
#if $param_max_number_of_peptides:
  -max_number_of_peptides $param_max_number_of_peptides
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
    <param name="param_svm_model" type="data" format="txt" optional="False" label="svm model in libsvm format (can be produced by PTModel)" help="(-svm_model) "/>
    <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) &lt;br&gt;"/>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
  </outputs>
  <help>**What it does**

predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PTPredict.html</help>
  <expand macro="references"/>
</tool>