comparison feature_linker_unlabeled.xml @ 4:1183846e70a1 draft

Uploaded

3:8fa16707e162

<tool id="openms_feature_linker_unlabeled" version="0.1.0" name="Feature Linker (Labeled)">
  <description>
    Groups corresponding features from multiple maps.
  </description>
  <macros>
    <import>macros.xml</import>

  <command interpreter="python">
    openms_wrapper.py --executable 'FeatureLinkedUnlabeled' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=$input1
out=$output
</configfile>
  </configfiles>
  <inputs>
    <conditional name="type">
      <param name="input_type" type="select" label="Input Type">
        <option value="featurexml">Features (FeatureXML)</option>
        <option value="consensusxml">Consensus (ConsensusXML)</option>
      </param>
      <when value="featurexml">
        <param format="featurexml" name="input1" type="data" label="Input Features" />
      </when>
      <when value="consensusxml">
        <param format="consensusxml" name="input1" type="data" label="Input Consensus" />
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="consensusxml" name="output" />
  </outputs>
  <help>

4:1183846e70a1

<tool id="openms_feature_linker_unlabeled" version="0.1.0" name="Feature Linker (Unlabeled)">
  <description>
    Groups corresponding features from multiple maps.
  </description>
  <macros>
    <import>macros.xml</import>

  <command interpreter="python">
    openms_wrapper.py --executable 'FeatureLinkedUnlabeled' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
in=${",".join(map(str, $inputs))}
out=$output
#if $type.input_type == "consensusxml"
$keep_subelements
#end if
$ignore_charge
$use_identifications
algorithm!second_nearest_gap=$second_nearest_gap
algorithm!distance_RT!max_difference=$rt_max_difference
algorithm!distance_MZ!max_difference=$mz_max_difference
algorithm!distance_MZ!unit=$mz_max_difference_unit
#if $advanced.specify
algorithm!distance_RT!weight=$advanced.rt_weight
algorithm!distance_MZ!weight=$advanced.mz_weight
algorithm!distance_intensity!weight=$advanced.intensity_weight
algorithm!distance_RT!exponent=$advanced.rt_exponent
algorithm!distance_MZ!exponent=$advanced.mz_exponent
algorithm!distance_intensity!exponent=$advanced.intensity_exponent
#end if
</configfile>
  </configfiles>
  <inputs>
    <expand macro="feature_linker_input" />
    <param name="second_nearest_gap" value="2" type="integer" label="Second Nearest Gap" help="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." />
    <expand macro="feature_linker_algorithm_options" />
  </inputs>
  <outputs>
    <data format="consensusxml" name="output" />
  </outputs>
  <help>