comparison MRMTransitionGroupPicker.xml @ 7:d88d659e7d2c draft

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

6:526a2e0e49e6

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

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

#end if
    #if $adv_opts.param_algorithm_compute_peak_quality:
  -algorithm:compute_peak_quality
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
    <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
    <param name="param_algorithm_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
    <param name="param_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>

    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Picks peaks in SRM/MRM chromatograms.


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

7:d88d659e7d2c

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

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

#end if
    #if $adv_opts.param_algorithm_compute_peak_quality:
  -algorithm:compute_peak_quality
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
    <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
    <param name="param_algorithm_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
    <param name="param_algorithm_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>

    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Picks peaks in SRM/MRM chromatograms.


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