annotate IDRTCalibration.xml @ 0:0f901d73c008 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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: [ID Processing]-->
<tool id="IDRTCalibration" name="IDRTCalibration" version="2.1.0">
  <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
  <macros>
    <token name="@EXECUTABLE@">IDRTCalibration</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDRTCalibration

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_calibrant_1_reference:
  -calibrant_1_reference $param_calibrant_1_reference
#end if
#if $param_calibrant_2_reference:
  -calibrant_2_reference $param_calibrant_2_reference
#end if
#if $param_calibrant_1_input:
  -calibrant_1_input $param_calibrant_1_input
#end if
#if $param_calibrant_2_input:
  -calibrant_2_input $param_calibrant_2_input
#end if
#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_calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file" help="(-calibrant_1_reference) "/>
    <param name="param_calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file" help="(-calibrant_2_reference) "/>
    <param name="param_calibrant_1_input" type="float" value="-1.0" label="The RT of the first calibrant in the input file" help="(-calibrant_1_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/>
    <param name="param_calibrant_2_input" type="float" value="-1.0" label="The RT of the second calibrant in the input file" help="(-calibrant_2_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" 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>Can be used to calibrate RTs of peptide hits linearly to standards.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html</help>
</tool>