comparison FeatureFinderMultiplex.xml @ 3:9ef0f56e82df draft

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

2:ca88bd28f116

<?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="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.1.0">
  <description>Determination of peak ratios in LC-MS data</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
    <import>macros.xml</import>
  </macros>

    #if $adv_opts.param_algorithm_averagine_similarity_scaling:
  -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
#end if
    #if $adv_opts.param_algorithm_knock_out:
  -algorithm:knock_out
#end if
    #if $adv_opts.param_algorithm_averagine_type:
  -algorithm:averagine_type
  #if " " in str($adv_opts.param_algorithm_averagine_type):
    "$adv_opts.param_algorithm_averagine_type"

          </valid>
        </sanitizer>
      </param>
      <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
      <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/>
      <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) ">
        <option value="peptide" selected="true">peptide</option>
        <option value="RNA">RNA</option>
        <option value="DNA">DNA</option>
      </param>

3:9ef0f56e82df

<?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="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0">
  <description>Determination of peak ratios in LC-MS data</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
    <import>macros.xml</import>
  </macros>

    #if $adv_opts.param_algorithm_averagine_similarity_scaling:
  -algorithm:averagine_similarity_scaling $adv_opts.param_algorithm_averagine_similarity_scaling
#end if
    #if $adv_opts.param_algorithm_knock_out:
  -algorithm:knock_out
#end if
    #if $adv_opts.param_algorithm_spectrum_type:
  -algorithm:spectrum_type
  #if " " in str($adv_opts.param_algorithm_spectrum_type):
    "$adv_opts.param_algorithm_spectrum_type"
  #else
    $adv_opts.param_algorithm_spectrum_type
  #end if
#end if
    #if $adv_opts.param_algorithm_averagine_type:
  -algorithm:averagine_type
  #if " " in str($adv_opts.param_algorithm_averagine_type):
    "$adv_opts.param_algorithm_averagine_type"

          </valid>
        </sanitizer>
      </param>
      <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
      <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/>
      <param name="param_algorithm_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Type of MS1 spectra in input mzML file" help="(-spectrum_type) 'automatic' determines the spectrum type directly from the input mzML file">
        <option value="profile">profile</option>
        <option value="centroid">centroid</option>
        <option value="automatic" selected="true">automatic</option>
      </param>
      <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) ">
        <option value="peptide" selected="true">peptide</option>
        <option value="RNA">RNA</option>
        <option value="DNA">DNA</option>
      </param>