| Previous changeset 12:9ec469ff191a (2019-03-22) Next changeset 14:3cf310697624 (2020-11-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 298cdc1df4609ae9353107dc803af0cf190ded7c" |
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modified:
msconvert.xml msconvert_macros.xml |
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| diff -r 9ec469ff191a -r 9b61227976d6 msconvert.xml --- a/msconvert.xml Fri Mar 22 14:18:29 2019 -0400 +++ b/msconvert.xml Sat Jul 25 18:13:58 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="msconvert" name="msconvert" version="@VERSION@.0"> +<tool id="msconvert" name="msconvert" version="@VERSION@.1"> <description>Convert and/or filter mass spectrometry files</description> <macros> <import>msconvert_macros.xml</import> |
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| diff -r 9ec469ff191a -r 9b61227976d6 msconvert_macros.xml --- a/msconvert_macros.xml Fri Mar 22 14:18:29 2019 -0400 +++ b/msconvert_macros.xml Sat Jul 25 18:13:58 2020 -0400 |
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| @@ -141,6 +141,9 @@ --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" @@ -376,6 +379,30 @@ <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> |