# HG changeset patch # User galaxyp # Date 1525761386 14400 # Node ID f3f6c32ab690e10afa201fa443850955733977d5 # Parent 9cbcf48bf60a93e72d4db369c48831e8e32d6ef6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f diff -r 9cbcf48bf60a -r f3f6c32ab690 msi_combine.xml --- a/msi_combine.xml Tue Apr 24 13:22:48 2018 -0400 +++ b/msi_combine.xml Tue May 08 02:36:26 2018 -0400 @@ -1,20 +1,21 @@ - + combine several mass spectrometry imaging datasets into one - bioconductor-cardinal + bioconductor-cardinal + r-ggplot2 0 & length(pixels(msidata_combined)) > 0) -{ - spectramatrix = spectra(msidata_combined) - rownames(spectramatrix) = mz(msidata_combined) - newmatrix = rbind(pixels(msidata_combined), spectramatrix) - write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") -}else{ - print("file has no features or pixels left") -} + if (length(features(msidata_combined))> 0 & length(pixels(msidata_combined)) > 0) + { + spectramatrix = spectra(msidata_combined) + rownames(spectramatrix) = mz(msidata_combined) + newmatrix = rbind(pixels(msidata_combined), spectramatrix) + write.table(newmatrix[2:nrow(newmatrix),], file="$matrixasoutput", quote = FALSE, row.names = TRUE, col.names=NA, sep = "\t") + }else{ + print("file has no features or pixels left") + } #end if ]]> @@ -107,13 +258,29 @@ - - - - - - + + + + + + + + + + + + + + + + + + + + + + @@ -125,6 +292,7 @@ + @@ -136,15 +304,36 @@ + + + + + + + + + + +