comparison msconvert_macros.xml @ 13:9b61227976d6 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c"

12:9ec469ff191a

      #if str($data_processing.ms2deisotope) == "true"
        --filter "MS2Deisotope"
      #end if


    ## SCAN INCLUSION/EXCLUSION FILTERS
      #if str($filtering.activation) != "false"
      --filter "activation $filtering.activation"
      #end if

        </when>
        <when value="false" />
      </conditional>

      <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />

    </section>


    <section name="filtering" title="Scan Inclusion/Exclusion Filters">

13:9b61227976d6

      #if str($data_processing.ms2deisotope) == "true"
        --filter "MS2Deisotope"
      #end if

      #if $data_processing.demultiplex.demultiplex_on
        --filter "demultiplex massError=$data_processing.demultiplex.massError$data_processing.demultiplex.massErrorUnits nnlsMaxIter=$data_processing.demultiplex.nnlsMaxIter nnlsEps=$data_processing.demultiplex.nnlsEps noWeighting=$data_processing.demultiplex.noWeighting demuxBlockExtra=$data_processing.demultiplex.demuxBlockExtra variableFill=$data_processing.demultiplex.variableFill noSumNormalize=$data_processing.demultiplex.noSumNormalize optimization=$data_processing.demultiplex.optimization interpolateRT=$data_processing.demultiplex.interpolateRT minWindowSize=$data_processing.demultiplex.minWindowSize"
      #end if

    ## SCAN INCLUSION/EXCLUSION FILTERS
      #if str($filtering.activation) != "false"
      --filter "activation $filtering.activation"
      #end if

        </when>
        <when value="false" />
      </conditional>

      <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" />

      <conditional name="demultiplex">
        <param name="demultiplex_on" type="boolean" label="Demultiplex overlapping or MSX spectra" help="Separates overlapping or MSX multiplexed spectra into several demultiplexed spectra by inferring from adjacent multiplexed spectra. Optionally handles variable fill times (for Thermo)" />
        <when value="true">
          <param name="massError" type="float" label="Demultiplex Mass Tolerance" value="10" />
          <param name="massErrorUnits" type="select" label="Units for Demultiplex Mass Tolerance">
            <option value="MZ">mz</option>
            <option value="PPM" selected="true">ppm</option>
          </param>
          <param name="nnlsMaxIter" type="integer" label="Maximum iterations for NNLS solve" value="50"/>
          <param name="nnlsEps" type="float" label="Epsilon value for convergence criterion of NNLS solver" value="1e-10"/>
          <param name="demuxBlockExtra" type="float" label="DemuxBlockExtra" help="Multiplier to expand or reduce the # of spectra considered when demultiplexing. If 0, a fully determined system of equations is built. If > 1.0, the number of rows included in the system is extended DemuxBlockExtra * (# scans in 1 duty cycle)" value="0"/>
          <param name="variableFill" type="boolean" truevalue="true" falsevalue="false" label="Allow fill times to vary for each scan window"/>
          <param name="noSumNormalize" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Normalize sums" help="After demultiplex solve, scale the sum of the intensities contributed from each of the input windows to match the non-demultiplexed intensity"/>
          <param name="optimization" type="select" label="Optimization" help="Optimizations can be applied when experimental design is known">
            <option value="none" selected="true">None</option>
            <option value="overlap_only">Overlap only</option>
          </param>
          <param name="interpolateRT" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Interpolate scan time"/>
          <param name="noWeighting" type="boolean" truevalue="false" falsevalue="true" checked="True" label="Weight nearby spectra higher" help="If true, weight the spectra nearby to the input spectrum more heavily in the solve than the outer ones. Weighting is only applied if interpolateRetentionTime is false"/>
          <param name="minWindowSize" type="float" label="Minimum window size" value="0.2"/>
        </when>
        <when value="false" />
      </conditional>

    </section>


    <section name="filtering" title="Scan Inclusion/Exclusion Filters">