view SpectraMerger.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="SpectraMerger" name="SpectraMerger" version="1.12.0">
  <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
  <macros>
    <token name="@EXECUTABLE@">SpectraMerger</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpectraMerger

-in ${param_in}
-out ${param_out}
-merging_method ${param_merging_method}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:block_method:ms_levels ${param_ms_levels}
-algorithm:block_method:rt_block_size ${param_rt_block_size}
-algorithm:block_method:rt_max_length ${param_rt_max_length}
-algorithm:precursor_method:mz_tolerance ${param_mz_tolerance}
-algorithm:precursor_method:rt_tolerance ${param_rt_tolerance}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:mz_binning_width ${adv_opts.param_mz_binning_width}
    -algorithm:mz_binning_width_unit ${adv_opts.param_mz_binning_width_unit}
    -algorithm:sort_blocks ${adv_opts.param_sort_blocks}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file." help="(-in)"/>
    <param name="param_merging_method" type="select" optional="True" value="block_method" label="Method of merging which should be used." help="(-merging_method)">
      <option value="precursor_method">precursor_method</option>
      <option value="block_method">block_method</option>
    </param>
    <param name="param_ms_levels" type="text" min="1" optional="True" size="20" value="1" label="Merge spectra of this level. All spectra with other MS levels remain untouched." help="(-ms_levels)"/>
    <param name="param_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up." help="(-rt_block_size)"/>
    <param name="param_rt_max_length" type="float" min="0.0" max="1e+11" optional="True" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)." help="(-rt_max_length)"/>
    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]." help="(-mz_tolerance)"/>
    <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]." help="(-rt_tolerance)"/>
    <expand macro="advanced_options">
      <param name="param_mz_binning_width" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of two peaks to be merged." help="(-mz_binning_width)"/>
      <param name="param_mz_binning_width_unit" type="select" optional="True" value="Da" label="Unit in which the distance between two peaks is given." help="(-mz_binning_width_unit)">
        <option value="Da">Da</option>
        <option value="ppm">ppm</option>
      </param>
      <param name="param_sort_blocks" type="select" optional="True" value="RT_ascending" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="(-sort_blocks)">
        <option value="RT_ascending">RT_ascending</option>
        <option value=" RT_descending"> RT_descending</option>
      </param>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output mzML file with merged spectra." format="mzML"/>
  </outputs>
  <help>**What it does**

Merges spectra (each MS level separately), increasing S/N ratios.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html

@REFERENCES@
</help>
</tool>