comparison TOFCalibration.xml @ 7:0d91d2be68be draft

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

6:f991f3776b65

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>TOFCalibration

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

#end if
    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window:
  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input peak or raw data file" help="(-in) "/>
    <param name="param_ext_calibrants" type="data" format="mzml" optional="False" label="input file containing the external calibrant spectra (peak or raw data)" help="(-ext_calibrants) "/>
    <param name="param_ref_masses" type="data" format="txt" optional="False" label="input file containing reference masses of the external calibrant spectra (one per line)" help="(-ref_masses) "/>
    <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants" help="(-tof_const) These can be either two or three constants &lt;br&gt;per set, depending on the conversion type. Either one set for all calibrant spectra  &lt;br&gt;(tab separated), or one for each spectrum. &lt;br&gt;For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)"/>

    <data name="param_out" format="mzml"/>
  </outputs>
  <help>Applies time of flight calibration.


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

7:0d91d2be68be

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[TOFCalibration

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

#end if
    #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window:
  -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input peak or raw data file" help="(-in) "/>
    <param name="param_ext_calibrants" type="data" format="mzml" optional="False" label="input file containing the external calibrant spectra (peak or raw data)" help="(-ext_calibrants) "/>
    <param name="param_ref_masses" type="data" format="txt" optional="False" label="input file containing reference masses of the external calibrant spectra (one per line)" help="(-ref_masses) "/>
    <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants" help="(-tof_const) These can be either two or three constants &lt;br&gt;per set, depending on the conversion type. Either one set for all calibrant spectra  &lt;br&gt;(tab separated), or one for each spectrum. &lt;br&gt;For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)"/>

    <data name="param_out" format="mzml"/>
  </outputs>
  <help>Applies time of flight calibration.


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