comparison PeakPickerIterative.xml @ 12:8dfefd19f00d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

11:b1dda5893efc

<?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: [Signal processing and preprocessing]-->
<tool id="PeakPickerIterative" name="PeakPickerIterative" version="2.2.0">
  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">PeakPickerIterative</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PeakPickerIterative

#if $param_in:
  -in $param_in
#end if
#if $param_out:

#end if
    #if $adv_opts.param_algorithm_check_width_internally:
  -algorithm:check_width_internally
#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_signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help="(-signal_to_noise_) "/>
    <param name="param_algorithm_peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="(-peak_width) In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
    <param name="param_algorithm_ms1_only" display="radio" type="boolean" truevalue="-algorithm:ms1_only" falsevalue="" checked="false" optional="True" label="Only do MS1" help="(-ms1_only) "/>

    <data name="param_out" format="mzml"/>
  </outputs>
  <help>Finds mass spectrometric peaks in profile mass spectra.


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

12:8dfefd19f00d

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Signal processing and preprocessing]-->
<tool id="PeakPickerIterative" name="PeakPickerIterative" version="2.3.0">
  <description>Finds mass spectrometric peaks in profile mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">PeakPickerIterative</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[PeakPickerIterative

#if $param_in:
  -in $param_in
#end if
#if $param_out:

#end if
    #if $adv_opts.param_algorithm_check_width_internally:
  -algorithm:check_width_internally
#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_signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help="(-signal_to_noise_) "/>
    <param name="param_algorithm_peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="(-peak_width) In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
    <param name="param_algorithm_ms1_only" display="radio" type="boolean" truevalue="-algorithm:ms1_only" falsevalue="" checked="false" optional="True" label="Only do MS1" help="(-ms1_only) "/>

    <data name="param_out" format="mzml"/>
  </outputs>
  <help>Finds mass spectrometric peaks in profile mass spectra.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_PeakPickerIterative.html</help>
</tool>