annotate FeatureFinderIsotopeWavelet.xml @ 3:1d8c27d75335 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

<?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: [Quantitation]-->
<tool id="FeatureFinderIsotopeWavelet" name="FeatureFinderIsotopeWavelet" version="2.2.0">
  <description>Detects two-dimensional features in LC-MS data.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderIsotopeWavelet</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderIsotopeWavelet

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_max_charge:
  -algorithm:max_charge $param_algorithm_max_charge
#end if
#if $param_algorithm_intensity_threshold:
  -algorithm:intensity_threshold $param_algorithm_intensity_threshold
#end if
#if $param_algorithm_hr_data:
  -algorithm:hr_data
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_intensity_type:
  -algorithm:intensity_type
  #if " " in str($adv_opts.param_algorithm_intensity_type):
    "$adv_opts.param_algorithm_intensity_type"
  #else
    $adv_opts.param_algorithm_intensity_type
  #end if
#end if
    #if $adv_opts.param_algorithm_check_ppm:
  -algorithm:check_ppm
#end if
    #if $adv_opts.param_algorithm_sweep_line_rt_votes_cutoff:
  -algorithm:sweep_line:rt_votes_cutoff $adv_opts.param_algorithm_sweep_line_rt_votes_cutoff
#end if
    #if $adv_opts.param_algorithm_sweep_line_rt_interleave:
  -algorithm:sweep_line:rt_interleave $adv_opts.param_algorithm_sweep_line_rt_interleave
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
    <param name="param_algorithm_max_charge" type="integer" min="1" optional="True" value="3" label="The maximal charge state to be considered" help="(-max_charge) "/>
    <param name="param_algorithm_intensity_threshold" type="float" value="-1.0" label="The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform" help="(-intensity_threshold) If you set intensity_threshold=-1, t' will be zero. &lt;br&gt;As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g"/>
    <param name="param_algorithm_hr_data" display="radio" type="boolean" truevalue="-algorithm:hr_data" falsevalue="" checked="false" optional="True" label="Must be true in case of high-resolution data, i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data," help="(-hr_data) e.g.). Please check a single MS scan out of your recording, if you are unsure"/>
    <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_intensity_type" display="radio" type="select" optional="False" value="ref" label="Determines the intensity type returned for the identified features" help="(-intensity_type) 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet)">
        <option value="ref" selected="true">ref</option>
        <option value="trans">trans</option>
        <option value="corrected">corrected</option>
      </param>
      <param name="param_algorithm_check_ppm" display="radio" type="boolean" truevalue="-algorithm:check_ppm" falsevalue="" checked="false" optional="True" label="Enables/disables a ppm test vs" help="(-check_ppm) the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied"/>
      <param name="param_algorithm_sweep_line_rt_votes_cutoff" type="integer" min="0" optional="True" value="5" label="Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature" help="(-rt_votes_cutoff) "/>
      <param name="param_algorithm_sweep_line_rt_interleave" type="integer" min="0" optional="True" value="1" label="Defines the maximum number of scans (w.r.t" help="(-rt_interleave) rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="featurexml"/>
  </outputs>
  <help>Detects two-dimensional features in LC-MS data.


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