changeset 13:9b61227976d6 draft

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

--- a/msconvert.xml	Fri Mar 22 14:18:29 2019 -0400
+++ b/msconvert.xml	Sat Jul 25 18:13:58 2020 -0400
@@ -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>

--- a/msconvert_macros.xml	Fri Mar 22 14:18:29 2019 -0400
+++ b/msconvert_macros.xml	Sat Jul 25 18:13:58 2020 -0400
@@ -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>