Mercurial > repos > galaxyp > cardinal_spectra_plots

comparison spectra_plots.xml @ 4:889c9e3a2526 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
author galaxyp
date Fri, 22 Mar 2019 08:08:11 -0400
parents 2553ba1fe625
children f64aadd66808
comparison
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3:2553ba1fe625 4:889c9e3a2526
1 <tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.2"> 1 <tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.3">
2 <description> 2 <description>
3 mass spectrometry imaging mass spectra plots 3 mass spectrometry imaging mass spectra plots
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
54 ## set NA to 0 otherwise plot function will not work 54 ## set NA to 0 otherwise plot function will not work
55 55
56 #if str($processed_cond.processed_file) == "processed": 56 #if str($processed_cond.processed_file) == "processed":
57 ##processed file needs to be converted into matrix to be able to replace NAs 57 ##processed file needs to be converted into matrix to be able to replace NAs
58 iData(msidata) <- iData(msidata)[] 58 iData(msidata) <- iData(msidata)[]
59 spectra(msidata)[is.na(spectra(msidata))] = 0
60 #else
61 spectra(msidata)[is.na(spectra(msidata))] = 0
62 #end if 59 #end if
60
61 spectra(msidata)[is.na(spectra(msidata))] = 0
63 62
64 ## run only if mz and pixels are > 0 63 ## run only if mz and pixels are > 0
65 64
66 if (ncol(msidata)>0 & nrow(msidata) >0){ 65 if (ncol(msidata)>0 & nrow(msidata) >0){
67 66