annotate RTPredict.xml @ 1:ad805b03ddf8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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="RTPredict" name="RTPredict" version="2.2.0">
  <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="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>RTPredict

#if $param_in_id:
  -in_id $param_in_id
#end if
#if $param_in_text:
  -in_text $param_in_text
#end if
#if $param_in_oligo_params:
  -in_oligo_params $param_in_oligo_params
#end if
#if $param_in_oligo_trainset:
  -in_oligo_trainset $param_in_oligo_trainset
#end if
#if $param_svm_model:
  -svm_model $param_svm_model
#end if
#if $param_total_gradient_time:
  -total_gradient_time $param_total_gradient_time
#end if
#if $param_out_id_file:
  -out_id:file $param_out_id_file
#end if
#if $param_out_id_positive:
  -out_id:positive $param_out_id_positive
#end if
#if $param_out_id_negative:
  -out_id:negative $param_out_id_negative
#end if
#if $param_out_text_file:
  -out_text:file $param_out_text_file
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_max_number_of_peptides:
  -max_number_of_peptides $adv_opts.param_max_number_of_peptides
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_out_id_rewrite_peptideidentification_rtmz:
  -out_id:rewrite_peptideidentification_rtmz
#end if
#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_in_oligo_params" type="data" format="paramXML" optional="True" label="input file with additional model parameters when using the OLIGO kernel" help="(-in_oligo_params) "/>
    <param name="param_in_oligo_trainset" type="data" format="txt" optional="True" label="input file with the used training dataset when using the OLIGO kernel" help="(-in_oligo_trainset) "/>
    <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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_out_id_rewrite_peptideidentification_rtmz" display="radio" type="boolean" truevalue="-out_id:rewrite_peptideidentification_rtmz" falsevalue="" 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_out_id_file" format="idxml"/>
    <data name="param_out_id_positive" format="idxml"/>
    <data name="param_out_id_negative" format="idxml"/>
    <data name="param_out_text_file" format="tabular"/>
  </outputs>
  <help>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</help>
</tool>