annotate MassTraceExtractor.xml @ 0:2fdd110666cb draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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 CTD2Galaxy.-->
<!--Proposed Tool Section: [Signal processing and preprocessing]-->
<tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.1.0">
  <description>Detects mass traces in centroided LC-MS data.</description>
  <macros>
    <token name="@EXECUTABLE@">MassTraceExtractor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MassTraceExtractor

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_type:
  -out_type
  #if " " in str($param_out_type):
    "$param_out_type"
  #else
    $param_out_type
  #end if
#end if
#if $param_algorithm_common_noise_threshold_int:
  -algorithm:common:noise_threshold_int $param_algorithm_common_noise_threshold_int
#end if
#if $param_algorithm_common_chrom_peak_snr:
  -algorithm:common:chrom_peak_snr $param_algorithm_common_chrom_peak_snr
#end if
#if $param_algorithm_common_chrom_fwhm:
  -algorithm:common:chrom_fwhm $param_algorithm_common_chrom_fwhm
#end if
#if $param_algorithm_mtd_mass_error_ppm:
  -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
#end if
#if $param_algorithm_mtd_reestimate_mt_sd:
  -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd
#end if
#if $param_algorithm_mtd_quant_method:
  -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method
#end if
#if $param_algorithm_epd_width_filtering:
  -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering
#end if
#if $param_algorithm_epd_enabled:
  -algorithm:epd:enabled $param_algorithm_epd_enabled
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
  -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion
#end if
    #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
  -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
#end if
    #if $adv_opts.param_algorithm_mtd_min_sample_rate:
  -algorithm:mtd:min_sample_rate $adv_opts.param_algorithm_mtd_min_sample_rate
#end if
    #if $adv_opts.param_algorithm_mtd_min_trace_length:
  -algorithm:mtd:min_trace_length $adv_opts.param_algorithm_mtd_min_trace_length
#end if
    #if $adv_opts.param_algorithm_mtd_max_trace_length:
  -algorithm:mtd:max_trace_length $adv_opts.param_algorithm_mtd_max_trace_length
#end if
    #if $adv_opts.param_algorithm_epd_min_fwhm:
  -algorithm:epd:min_fwhm $adv_opts.param_algorithm_epd_min_fwhm
#end if
    #if $adv_opts.param_algorithm_epd_max_fwhm:
  -algorithm:epd:max_fwhm $adv_opts.param_algorithm_epd_max_fwhm
#end if
    #if $adv_opts.param_algorithm_epd_masstrace_snr_filtering:
  -algorithm:epd:masstrace_snr_filtering
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input centroided mzML file" help="(-in) "/>
    <param name="param_out_type" display="radio" type="select" optional="True" label="output file type -- default: determined from file extension or content" help="(-out_type) ">
      <option value="featureXML">featureXML</option>
      <option value="consensusXML">consensusXML</option>
    </param>
    <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
    <param name="param_algorithm_common_chrom_peak_snr" type="float" value="3.0" label="Minimum signal-to-noise a mass trace should have" help="(-chrom_peak_snr) "/>
    <param name="param_algorithm_common_chrom_fwhm" type="float" value="5.0" label="Expected chromatographic peak width (in seconds)" help="(-chrom_fwhm) "/>
    <param name="param_algorithm_mtd_mass_error_ppm" type="float" value="20.0" label="Allowed mass deviation (in ppm)" help="(-mass_error_ppm) "/>
    <param name="param_algorithm_mtd_reestimate_mt_sd" display="radio" type="select" optional="False" value="true" label="Enables dynamic re-estimation of m/z variance during mass trace collection stage" help="(-reestimate_mt_sd) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_algorithm_mtd_quant_method" display="radio" type="select" optional="False" value="area" label="Method of quantification for mass traces" help="(-quant_method) For LC data 'area' is recommended, 'median' for direct injection data">
      <option value="area" selected="true">area</option>
      <option value="median">median</option>
    </param>
    <param name="param_algorithm_epd_width_filtering" display="radio" type="select" optional="False" value="fixed" label="Enable filtering of unlikely peak widths" help="(-width_filtering) The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution">
      <option value="off">off</option>
      <option value="fixed" selected="true">fixed</option>
      <option value="auto">auto</option>
    </param>
    <param name="param_algorithm_epd_enabled" display="radio" type="select" optional="False" value="true" label="Enables/disables the chromatographic peak detection of mass traces" help="(-enabled) ">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <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_mtd_trace_termination_criterion" display="radio" type="select" optional="False" value="outlier" label="Termination criterion for the extension of mass traces" help="(-trace_termination_criterion) In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold">
        <option value="outlier" selected="true">outlier</option>
        <option value="sample_rate">sample_rate</option>
      </param>
      <param name="param_algorithm_mtd_trace_termination_outliers" type="integer" value="5" label="Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached" help="(-trace_termination_outliers) "/>
      <param name="param_algorithm_mtd_min_sample_rate" type="float" value="0.5" label="Minimum fraction of scans along the mass trace that must contain a peak" help="(-min_sample_rate) "/>
      <param name="param_algorithm_mtd_min_trace_length" type="float" value="5.0" label="Minimum expected length of a mass trace (in seconds)" help="(-min_trace_length) "/>
      <param name="param_algorithm_mtd_max_trace_length" type="float" value="-1.0" label="Maximum expected length of a mass trace (in seconds)" help="(-max_trace_length) Set to a negative value to disable maximal length check during mass trace detection"/>
      <param name="param_algorithm_epd_min_fwhm" type="float" value="3.0" label="Minimum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-min_fwhm) Ignored if parameter width_filtering is off or auto"/>
      <param name="param_algorithm_epd_max_fwhm" type="float" value="60.0" label="Maximum full-width-at-half-maximum of chromatographic peaks (in seconds)" help="(-max_fwhm) Ignored if parameter width_filtering is off or auto"/>
      <param name="param_algorithm_epd_masstrace_snr_filtering" display="radio" type="boolean" truevalue="-algorithm:epd:masstrace_snr_filtering" falsevalue="" checked="false" optional="True" label="Apply post-filtering by signal-to-noise ratio after smoothing" help="(-masstrace_snr_filtering) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Detects mass traces in centroided LC-MS data.


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