annotate SpectraMerger.xml @ 6:f8717535fbe3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

<?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="SpectraMerger" name="SpectraMerger" version="2.3.0">
  <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="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SpectraMerger

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_merging_method:
  -merging_method
  #if " " in str($param_merging_method):
    "$param_merging_method"
  #else
    $param_merging_method
  #end if
#end if
#if $param_algorithm_average_gaussian_spectrum_type:
  -algorithm:average_gaussian:spectrum_type
  #if " " in str($param_algorithm_average_gaussian_spectrum_type):
    "$param_algorithm_average_gaussian_spectrum_type"
  #else
    $param_algorithm_average_gaussian_spectrum_type
  #end if
#end if
#if $param_algorithm_average_gaussian_ms_level:
  -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
#end if
#if $param_algorithm_average_gaussian_rt_FWHM:
  -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
#end if
#if $param_algorithm_average_tophat_spectrum_type:
  -algorithm:average_tophat:spectrum_type
  #if " " in str($param_algorithm_average_tophat_spectrum_type):
    "$param_algorithm_average_tophat_spectrum_type"
  #else
    $param_algorithm_average_tophat_spectrum_type
  #end if
#end if
#if $param_algorithm_average_tophat_ms_level:
  -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
#end if
#if $param_algorithm_average_tophat_rt_range:
  -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
#end if
#if $param_algorithm_average_tophat_rt_unit:
  -algorithm:average_tophat:rt_unit
  #if " " in str($param_algorithm_average_tophat_rt_unit):
    "$param_algorithm_average_tophat_rt_unit"
  #else
    $param_algorithm_average_tophat_rt_unit
  #end if
#end if

#if $rep_param_algorithm_block_method_ms_levels:
-algorithm:block_method:ms_levels
  #for token in $rep_param_algorithm_block_method_ms_levels:
    #if " " in str(token):
      "$token.param_algorithm_block_method_ms_levels"
    #else
      $token.param_algorithm_block_method_ms_levels
    #end if
  #end for
#end if
#if $param_algorithm_block_method_rt_block_size:
  -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size
#end if
#if $param_algorithm_block_method_rt_max_length:
  -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length
#end if
#if $param_algorithm_precursor_method_mz_tolerance:
  -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance
#end if
#if $param_algorithm_precursor_method_rt_tolerance:
  -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_mz_binning_width:
  -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
#end if
    #if $adv_opts.param_algorithm_mz_binning_width_unit:
  -algorithm:mz_binning_width_unit
  #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit):
    "$adv_opts.param_algorithm_mz_binning_width_unit"
  #else
    $adv_opts.param_algorithm_mz_binning_width_unit
  #end if
#end if
    #if $adv_opts.param_algorithm_sort_blocks:
  -algorithm:sort_blocks
  #if " " in str($adv_opts.param_algorithm_sort_blocks):
    "$adv_opts.param_algorithm_sort_blocks"
  #else
    $adv_opts.param_algorithm_sort_blocks
  #end if
#end if
    #if $adv_opts.param_algorithm_average_gaussian_cutoff:
  -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff
#end if
#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" display="radio" type="select" optional="False" value="average_gaussian" label="Method of merging which should be used" help="(-merging_method) ">
      <option value="average_gaussian" selected="true">average_gaussian</option>
      <option value="average_tophat">average_tophat</option>
      <option value="precursor_method">precursor_method</option>
      <option value="block_method">block_method</option>
    </param>
    <param name="param_algorithm_average_gaussian_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
      <option value="profile">profile</option>
      <option value="centroid">centroid</option>
      <option value="automatic" selected="true">automatic</option>
    </param>
    <param name="param_algorithm_average_gaussian_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
    <param name="param_algorithm_average_gaussian_rt_FWHM" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help="(-rt_FWHM) "/>
    <param name="param_algorithm_average_tophat_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Spectrum type of the MS level to be averaged" help="(-spectrum_type) ">
      <option value="profile">profile</option>
      <option value="centroid">centroid</option>
      <option value="automatic" selected="true">automatic</option>
    </param>
    <param name="param_algorithm_average_tophat_ms_level" type="integer" min="1" optional="True" value="1" label="Average spectra of this level" help="(-ms_level) All other spectra remain unchanged"/>
    <param name="param_algorithm_average_tophat_rt_range" type="float" min="0.0" max="1e+11" optional="True" value="5.0" label="RT range to be averaged over, i.e" help="(-rt_range) +/-(RT range)/2 from each spectrum"/>
    <param name="param_algorithm_average_tophat_rt_unit" display="radio" type="select" optional="False" value="scans" label="Unit for RT range" help="(-rt_unit) ">
      <option value="scans" selected="true">scans</option>
      <option value="seconds">seconds</option>
    </param>
    <repeat name="rep_param_algorithm_block_method_ms_levels" min="0" max="1" title="param_algorithm_block_method_ms_levels">
      <param name="param_algorithm_block_method_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="Merge spectra of this level" help="(-ms_levels) All spectra with other MS levels remain untouched">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_algorithm_block_method_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_algorithm_block_method_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_algorithm_precursor_method_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_algorithm_precursor_method_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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_algorithm_mz_binning_width" type="float" min="0.0" optional="True" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="(-mz_binning_width) Closer data points or peaks will be merged"/>
      <param name="param_algorithm_mz_binning_width_unit" display="radio" type="select" optional="False" value="ppm" label="Unit in which the distance between two data points or peaks is given" help="(-mz_binning_width_unit) ">
        <option value="Da">Da</option>
        <option value="ppm" selected="true">ppm</option>
      </param>
      <param name="param_algorithm_sort_blocks" display="radio" type="select" optional="False" value="RT_ascending" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="(-sort_blocks) ">
        <option value="RT_ascending" selected="true">RT_ascending</option>
        <option value=" RT_descending"> RT_descending</option>
      </param>
      <param name="param_algorithm_average_gaussian_cutoff" type="float" min="0.0" max="1.0" optional="True" value="0.01" label="Intensity cutoff for Gaussian" help="(-cutoff) The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="mzml"/>
  </outputs>
  <help>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</help>
</tool>