Mercurial > repos > galaxyp > msi_combine
changeset 4:c1c0618fe430 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
| author | galaxyp |
|---|---|
| date | Tue, 19 Jun 2018 18:04:30 -0400 |
| parents | f07413fa9b58 |
| children | 49c4a97e7e3a |
| files | msi_combine.xml test-data/112_auto_combined_QC.pdf test-data/123_combined_QC.pdf test-data/123_no_combi_QC.pdf test-data/12_combined_QC.pdf |
| diffstat | 5 files changed, 10 insertions(+), 4 deletions(-) [+] |
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--- a/msi_combine.xml Mon Jun 11 17:31:11 2018 -0400 +++ b/msi_combine.xml Tue Jun 19 18:04:30 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.1"> +<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.2"> <description> combine several mass spectrometry imaging datasets into one </description> @@ -68,7 +68,7 @@ #for $i, $infile in enumerate($infiles): #if $infile.ext == 'imzml' - msidata_$i <- readImzML('infile_${i}') + msidata_$i <- readImzML('infile_${i}', mass.accuracy=$accuracy, units.accuracy = "$units") #elif $infile.ext == 'analyze75' msidata_$i <- readAnalyze('infile_${i}') #else @@ -209,7 +209,8 @@ theme_bw()+ theme(text=element_text(family="ArialMT", face="bold", size=15))+ theme(legend.position="bottom",legend.direction="vertical")+ - guides(fill=guide_legend(ncol=4,byrow=TRUE)) + theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 6))+ + guides(fill=guide_legend(ncol=5,byrow=TRUE)) coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean) coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) for(file_count in 1:nrow(coord_labels)) @@ -239,8 +240,13 @@ </configfiles> <inputs> <param name="infiles" type="data" multiple="true" format="imzml,rdata,analyze75" - label="MSI rawdata as imzml, analyze7.5 or Cardinal MSImageSet saved as RData" + 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="combine_conditional"> <param name="combine_method" type="select" label="Select the way you want to combine multiple files" help="More detailed help can be found in the help section at the bottom"> <option value="automatic_combine" selected="True" >automatic combination</option>