comparison MRMMapper.xml @ 7:305bf5edf3ce draft

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

6:c0388664d0fe

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

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

#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="mzml" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in) "/>
    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
    <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance) "/>
    <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance) "/>

    <data name="param_out" format="mzml"/>
  </outputs>
  <help>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)


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

7:305bf5edf3ce

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

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

#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="mzml" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in) "/>
    <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
    <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance) "/>
    <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance) "/>

    <data name="param_out" format="mzml"/>
  </outputs>
  <help>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)


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