comparison PTPredict.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

3:ec62782f6c68

<?xml version='1.0' encoding='UTF-8'?>
<tool id="PTPredict" name="PTPredict" version="1.12.0">
  <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

-in ${param_in}
-out ${param_out}
-svm_model ${param_svm_model}
-max_number_of_peptides ${param_max_number_of_peptides}
-threads \${GALAXY_SLOTS:-24} 
</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).#br#" help="(-max_number_of_peptides)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file#br#" 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

@REFERENCES@
</help>
</tool>

4:6ead64a594bd

<?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="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="references"/>
    <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 format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param format="txt" help="(-svm_model) " label="svm model in libsvm format (can be produced by PTModel)" name="param_svm_model" optional="False" type="data"/>
      <param help="(-max_number_of_peptides) &lt;br&gt;" label="the maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory)" name="param_max_number_of_peptides" type="integer" value="100000"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
    </outputs>
    <help>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>
  </tool>