Mercurial > repos > galaxyp > msi_preprocessing
changeset 6:d3fd539f477e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_preprocessing commit 6d877681b6188999b4f5abb1843b420078b71b92
| author | galaxyp |
|---|---|
| date | Thu, 21 Jun 2018 16:45:55 -0400 |
| parents | 2fccfd11360d |
| children | 1a3d477bc54a |
| files | msi_preprocessing.xml test-data/preprocessing_results1.RData test-data/preprocessing_results1.pdf test-data/preprocessing_results2.pdf test-data/preprocessing_results3.RData test-data/preprocessing_results3.pdf test-data/preprocessing_results4.RData test-data/preprocessing_results4.pdf test-data/preprocessing_results5.RData test-data/preprocessing_results5.pdf |
| diffstat | 10 files changed, 22 insertions(+), 10 deletions(-) [+] |
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--- a/msi_preprocessing.xml Tue Jun 19 18:08:01 2018 -0400 +++ b/msi_preprocessing.xml Thu Jun 21 16:45:55 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.2"> +<tool id="mass_spectrometry_imaging_preprocessing" name="MSI preprocessing" version="1.10.0.3"> <description> mass spectrometry imaging preprocessing </description> @@ -6,7 +6,6 @@ <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> <requirement type="package" version="2.2.1">r-gridextra</requirement> <requirement type="package" version="0.20-35">r-lattice</requirement> - <!--requirement type="package" version="3.34.9">bioconductor-limma</requirement--> </requirements> <command detect_errors="exit_code"> <![CDATA[ @@ -34,10 +33,13 @@ library(Cardinal) library(gridExtra) library(lattice) -###library(limma) #if $infile.ext == 'imzml' - msidata <- readImzML('infile', mass.accuracy=$accuracy, units.accuracy = "$units") + #if str($processed_cond.processed_file) == "processed": + msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + #else + msidata <- readImzML('infile') + #end if #elif $infile.ext == 'analyze75' msidata = readAnalyze('infile') #else @@ -417,11 +419,20 @@ <param name="infile" type="data" format="imzml,rdata,danalyze75" label="MSI data as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" help="load imzml and ibd file by uploading composite datatype imzml"/> - <param name="accuracy" type="float" value="50" label="Only for processed imzML files: enter mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> - <param name="units" display="radio" type="select" label="Only for processed imzML files: unit of the mass accuracy" help="either m/z or ppm"> - <option value="mz" >mz</option> - <option value="ppm" selected="True" >ppm</option> - </param> + <conditional name="processed_cond"> + <param name="processed_file" type="select" label="Is the input file a processed imzML file "> + <option value="no_processed" selected="True">not a processed imzML</option> + <option value="processed">processed imzML</option> + </param> + <when value="no_processed"/> + <when value="processed"> + <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> + <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> + <option value="mz" >mz</option> + <option value="ppm" selected="True" >ppm</option> + </param> + </when> + </conditional> <repeat name="methods" title="Preprocessing" min="1" max="50"> <conditional name="methods_conditional"> <param name="preprocessing_method" type="select" label="Select the preprocessing methods you want to apply"> @@ -501,7 +512,7 @@ <param name="units_diffalignment" type="select" display = "radio" optional = "False" label="units"> <option value="ppm" selected="True">ppm</option> - <option value="Da">Da</option> + <option value="Da">m/z</option> </param> </when> <when value="DP"> @@ -790,6 +801,7 @@ - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value - Peak filtering: works only on centroided data (after peak picking and alignment or data reduction with peak filtering), removes peaks that occur only in a small proportion of pixels. If not sure which cutoff to chose run qualitycontrol first and decide according to the zero value plot. - Data reduction: binning, resampling or peak filtering to reduce data +- Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. Output: