view FeatureLinkerUnlabeled.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

<?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="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.0.0">
    <description>Groups corresponding features from multiple maps.</description>
    <macros>
      <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>FeatureLinkerUnlabeled

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_keep_subelements:
  -keep_subelements
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_second_nearest_gap:
  -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap
#end if
#if $param_algorithm_use_identifications:
  -algorithm:use_identifications
#end if
#if $param_algorithm_ignore_charge:
  -algorithm:ignore_charge
#end if
#if $param_algorithm_distance_RT_max_difference:
  -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference
#end if
#if $param_algorithm_distance_MZ_max_difference:
  -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference
#end if
#if $param_algorithm_distance_MZ_unit:
  -algorithm:distance_MZ:unit
  #if &quot; &quot; in str($param_algorithm_distance_MZ_unit):
    &quot;$param_algorithm_distance_MZ_unit&quot;
  #else
    $param_algorithm_distance_MZ_unit
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_distance_RT_exponent:
  -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent
#end if
    #if $adv_opts.param_algorithm_distance_RT_weight:
  -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight
#end if
    #if $adv_opts.param_algorithm_distance_MZ_exponent:
  -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent
#end if
    #if $adv_opts.param_algorithm_distance_MZ_weight:
  -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight
#end if
    #if $adv_opts.param_algorithm_distance_intensity_exponent:
  -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent
#end if
    #if $adv_opts.param_algorithm_distance_intensity_weight:
  -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
#end if
#end if
</command>
    <inputs>
      <param format="xml,consensusxml" help="(-in) " label="input files separated by blanks" multiple="true" name="param_in" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param checked="false" falsevalue="" help="(-keep_subelements) " label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" name="param_keep_subelements" optional="True" truevalue="-keep_subelements" type="boolean"/>
      <param help="(-second_nearest_gap) " label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" min="1.0" name="param_algorithm_second_nearest_gap" optional="True" type="float" value="2.0"/>
      <param checked="false" falsevalue="" help="(-use_identifications) " label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" name="param_algorithm_use_identifications" optional="True" truevalue="-algorithm:use_identifications" type="boolean"/>
      <param checked="false" falsevalue="" help="(-ignore_charge) " label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" name="param_algorithm_ignore_charge" optional="True" truevalue="-algorithm:ignore_charge" type="boolean"/>
      <param help="(-max_difference) " label="Never pair features with a larger RT distance (in seconds)" min="0.0" name="param_algorithm_distance_RT_max_difference" optional="True" type="float" value="100.0"/>
      <param help="(-max_difference) " label="Never pair features with larger m/z distance (unit defined by 'unit')" min="0.0" name="param_algorithm_distance_MZ_max_difference" optional="True" type="float" value="0.3"/>
      <param help="(-unit) " label="Unit of the 'max_difference' paramete" name="param_algorithm_distance_MZ_unit" optional="True" type="select" value="Da">
        <option value="Da">Da</option>
        <option value="ppm">ppm</option>
      </param>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param help="(-exponent) " label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_RT_exponent" optional="True" type="float" value="1.0"/>
        <param help="(-weight) " label="Final RT distances are weighted by this facto" min="0.0" name="param_algorithm_distance_RT_weight" optional="True" type="float" value="1.0"/>
        <param help="(-exponent) " label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_MZ_exponent" optional="True" type="float" value="2.0"/>
        <param help="(-weight) " label="Final m/z distances are weighted by this facto" min="0.0" name="param_algorithm_distance_MZ_weight" optional="True" type="float" value="1.0"/>
        <param help="(-exponent) " label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" min="0.0" name="param_algorithm_distance_intensity_exponent" optional="True" type="float" value="1.0"/>
        <param help="(-weight) " label="Final intensity distances are weighted by this facto" min="0.0" name="param_algorithm_distance_intensity_weight" optional="True" type="float" value="0.0"/>
      </expand>
    </inputs>
    <outputs>
      <data format="consensusxml" name="param_out"/>
    </outputs>
    <help>Groups corresponding features from multiple maps.


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