annotate FeatureLinkerLabeled.xml @ 0:2fe5ef9f1760 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: [Map Alignment]-->
<tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="2.1.0">
  <description>Groups corresponding isotope-labeled features in a feature map.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureLinkerLabeled</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureLinkerLabeled

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_algorithm_rt_estimate:
  -algorithm:rt_estimate $param_algorithm_rt_estimate
#end if
#if $param_algorithm_rt_pair_dist:
  -algorithm:rt_pair_dist $param_algorithm_rt_pair_dist
#end if
#if $param_algorithm_rt_dev_low:
  -algorithm:rt_dev_low $param_algorithm_rt_dev_low
#end if
#if $param_algorithm_rt_dev_high:
  -algorithm:rt_dev_high $param_algorithm_rt_dev_high
#end if

#if $rep_param_algorithm_mz_pair_dists:
-algorithm:mz_pair_dists
  #for token in $rep_param_algorithm_mz_pair_dists:
    #if " " in str(token):
      "$token.param_algorithm_mz_pair_dists"
    #else
      $token.param_algorithm_mz_pair_dists
    #end if
  #end for
#end if
#if $param_algorithm_mz_dev:
  -algorithm:mz_dev $param_algorithm_mz_dev
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_mrm:
  -algorithm:mrm
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featurexml" optional="False" label="Input file" help="(-in) "/>
    <param name="param_algorithm_rt_estimate" display="radio" type="select" optional="False" value="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="(-rt_estimate) Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <param name="param_algorithm_rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help="(-rt_pair_dist) "/>
    <param name="param_algorithm_rt_dev_low" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation below optimal retention time distance" help="(-rt_dev_low) "/>
    <param name="param_algorithm_rt_dev_high" type="float" min="0.0" optional="True" value="15.0" label="maximum allowed deviation above optimal retention time distance" help="(-rt_dev_high) "/>
    <repeat name="rep_param_algorithm_mz_pair_dists" min="0" max="1" title="param_algorithm_mz_pair_dists">
      <param name="param_algorithm_mz_pair_dists" type="text" size="30" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, ." help="(-mz_pair_dists) by division through charge)">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_algorithm_mz_dev" type="float" min="0.0" optional="True" value="0.05" label="maximum allowed deviation from optimal m/z distance" help="(-mz_dev) "/>
    <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_mrm" display="radio" type="boolean" truevalue="-algorithm:mrm" falsevalue="" checked="false" optional="True" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help="(-mrm) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="consensusxml"/>
  </outputs>
  <help>Groups corresponding isotope-labeled features in a feature map.


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