annotate FeatureFinderMRM.xml @ 3:7dcc6299da76 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: [Quantitation]-->
<tool id="FeatureFinderMRM" name="FeatureFinderMRM" version="2.2.0">
  <description>Detects two-dimensional features in LC-MS data.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMRM</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderMRM

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_min_rt_distance:
  -algorithm:min_rt_distance $param_algorithm_min_rt_distance
#end if
#if $param_algorithm_min_signal_to_noise_ratio:
  -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
  -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
#end if
    #if $adv_opts.param_algorithm_write_debug_files:
  -algorithm:write_debug_files
#end if
    #if $adv_opts.param_algorithm_resample_traces:
  -algorithm:resample_traces
#end if
    #if $adv_opts.param_algorithm_write_debuginfo:
  -algorithm:write_debuginfo
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
    <param name="param_algorithm_min_rt_distance" type="float" min="0.0" optional="True" value="10.0" label="Minimal distance of MRM features in seconds" help="(-min_rt_distance) "/>
    <param name="param_algorithm_min_signal_to_noise_ratio" type="float" min="0.0" optional="True" value="2.0" label="Minimal S/N ratio a peak must have to be taken into account" help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise"/>
    <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) "/>
      <param name="param_algorithm_min_num_peaks_per_feature" type="integer" min="1" optional="True" value="5" label="Minimal number of peaks which are needed for a single feature" help="(-min_num_peaks_per_feature) "/>
      <param name="param_algorithm_write_debug_files" display="radio" type="boolean" truevalue="-algorithm:write_debug_files" falsevalue="" checked="false" optional="True" label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" help="(-write_debug_files) "/>
      <param name="param_algorithm_resample_traces" display="radio" type="boolean" truevalue="-algorithm:resample_traces" falsevalue="" checked="false" optional="True" label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" help="(-resample_traces) "/>
      <param name="param_algorithm_write_debuginfo" display="radio" type="boolean" truevalue="-algorithm:write_debuginfo" falsevalue="" checked="false" optional="True" label="If set to true, debug messages are written, the output can be somewhat lengthy" help="(-write_debuginfo) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Detects two-dimensional features in LC-MS data.


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