annotate macros.xml @ 6:42b843627623 draft default tip

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<macros>
  <macro name="stdio">
    <stdio>
      <exit_code range="1:"  level="fatal"   description="Error running OpenMS tool." />
    </stdio>
  </macro>
  <macro name="requires">
    <requirements>
      <requirement type="package">openms</requirement>
      <yield />
    </requirements>
  </macro>
  <macro name="sampling_rate_param">
    <param name="sampling_rate_param" label="Sampling Rate" help="New sampling rate in m/z dimension." value="0.1" type="float" />
  </macro>
  <macro name="id_inputs">
    <param name="input1" label="Input Peak List (mzML)" type="data" format="mzml" />
    <param name="database" label="Database" type="data" format="fasta" />
  </macro>
  <macro name="id_outputs">
    <outputs>
      <data format="idxml" name="out" />
    </outputs>
  </macro>
  <macro name="precursor_mass_tolerance_param">
    <param name="precursor_mass_tolerance" label="Precursor Mass Tolerance" value="1.5" type="float" />
  </macro>
  <macro name="precursor_mass_tolerance_unit_param">
    <param name="precursor_mass_tolerance_unit" label="Precursor Mass Tolerance Units" type="select">
      <option value="Da" selected="true">Daltons</option>
      <option value="ppm">ppm</option>
    </param>
  </macro>
  <macro name="fragment_mass_tolerance_param">
    <param name="fragment_mass_tolerance" label="Fragment Mass Tolerance" value="0.3" type="float" />
  </macro>
  <macro name="fragment_mass_tolerance_unit_param">
    <param name="fragment_mass_tolerance_unit" label="Fragment Mass Tolerance Units" type="select">
      <option value="Da" selected="true">Daltons</option>
      <option value="ppm">ppm</option>
    </param>
  </macro>
  <macro name="fixed_modifications_param">
    <param name="fixed_modifications" type="select" label="Fixed Modification" multiple="true">
      <options from_file="openms_mods.loc">
        <column name="name" index="0" />
        <column name="value" index="0" />
      </options>
    </param>
  </macro>
  <macro name="variable_modifications_param">
    <param name="variable_modifications" type="select" label="Variable Modification" multiple="true">
      <options from_file="openms_mods.loc">
        <column name="name" index="0" />
        <column name="value" index="0" />
      </options>
    </param>
  </macro>
  <macro name="precursor_charge_params">
    <param name="min_precursor_charge" label="Minimum Precursor Charge" value="1" type="integer" />
    <param name="max_precursor_charge" label="Maximum Precursor Charge" value="4" type="integer" />
  </macro>
  <macro name="raw_feature_finder_params">
    <param name="rt_threshold" type="float" value="30" label="RT Threshold" help="Upper bound for the retention time [s] over which a characteristic peptide elutes." />
    <param name="rt_min" type="float" value="0" label="RT Minimum" help="Lower bound for the retention time [s]." />
    <param name="intensity_cutoff" type="float" value="10000" label="Intensity Cutoff" help="Lower bound for the intensity of isotopic peaks in a SILAC pattern." />
    <param name="intensity_correlation" type="float" value="0.7" label="Intensity Correlation" help="Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate." />
    <param name="model_deviation" type="float" value="3" label="Model Deviation" help="Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) &lt; observed_ratio &lt; ( theoretic_ratio * model_deviation )." />
    <param name="min_charge" type="integer" value="2" label="Minimum Charge" />
    <param name="max_charge" type="integer" value="4" label="Maximum Charge" />
    <param name="min_peaks_per_peptide" type="integer" value="3" label="Minimum Number of Peaks Per Peptide" />
    <param name="max_peaks_per_peptide" type="integer" value="5" label="Maximum Number of Peaks Per Peptide" />
  </macro>
  <macro name="map_input">
  </macro>
  <macro name="map_output">
    <data format="consensusxml" name="map_output">
      <change_format>
        <when input="input_type" value="featurexml" format="featurexml" />
      </change_format>
    </data>
  </macro>
  <macro name="aligner_model">
    <conditional name="model">
      <param name="model_type" type="select" label="Model Type">
        <option value="linear">Linear</option>
        <option value="b_spline" selected="true">Smoothing spline (non-linear)</option>
        <option value="interpolated">Interpolated</option>
      </param>
      <when value="linear">
        <!-- TODO: Add symmetric_regression -->
      </when>
      <when value="b_spline">
        <!-- TODO: Add num_breakpoints, break_positions -->
      </when>
      <when value="interpolated">
        <param name="interpolation_type" type="select" label="Interpolation Type">
          <option value="cspline" selected="true">cspline</option>
          <option value="linear">linear</option>
          <option value="akima">akima</option>
        </param>
      </when>
    </conditional>
  </macro>
  <macro name="feature_linker_input">
    <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="inputs" type="data" label="Input Features" multiple="true" />
      </when>
      <when value="consensusxml">
        <param format="consensusxml" name="inputs" type="data" label="Input Consensus" multiple="true" />
        <param name="keep_subelements" type="boolean" label="Transfer sub-features of the inputs to the output." truevalue="keep_subelements=true" falsevalue="" />        
      </when>
    </conditional>
  </macro>
  <macro name="feature_linker_algorithm_options">
    <param name="use_identifications" type="boolean" truevalue="algorithm!use_identifications=true" falsevalue="" label="Use Identifications" checked="false" help="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." />
    <param name="ignore_charge" type="boolean" truevalue="algorithm!ignore_charge=true" falsevalue="" label="Use Charge" help="Compare features normally even if their charge states are different." checked="false" />    
    <param name="rt_max_difference" type="float" label="Max Difference (RT)" value="100" help="Maximum allowed difference in RT in seconds." />
    <param name="mz_max_difference" type="float" label="Max Difference (m/z)" value="0.3" help="Maximum allowed difference in m/z" />
    <param name="mz_max_difference_unit" type="select" label="Max Difference Units (m/z)">
      <option value="Da" selected="true">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>
    <conditional name="advanced">
      <param name="specify" type="boolean" label="Specify advanced exponents and weights for distances (RT, m/z, and intensity)" />
      <when value="true">
        <param name="rt_exponent" label="RT Exponent" help="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
        <param name="mz_exponent" label="m/z Exponent" help="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
        <param name="intensity_exponent" label="Intensity Exponent" help="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" type="float" value="1" />
        <param name="rt_weight" label="RT Exponent" help="RT distances are weighted by this factor" type="float" value="1" />
        <param name="mz_weight" label="m/z Exponent" help="m/z distances are weighted by this factor" type="float" value="2" />
        <param name="intensity_weight" label="Intensity Exponent" help="Distances based on relative intensity are weighted by this factor" type="float" value="0" />
      </when>
      <when value="false">
      </when>
    </conditional>
  </macro>
</macros>