Mercurial > repos > galaxyp > cardinal_spectra_plots
diff spectra_plots.xml @ 1:1d9931768896 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
| author | galaxyp |
|---|---|
| date | Thu, 25 Oct 2018 07:30:24 -0400 |
| parents | 9c03e7a617cd |
| children | 3642ed221eb2 |
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--- a/spectra_plots.xml Mon Oct 01 01:08:16 2018 -0400 +++ b/spectra_plots.xml Thu Oct 25 07:30:24 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.0"> +<tool id="cardinal_spectra_plots" name="MSI plot spectra" version="@VERSION@.1"> <description> mass spectrometry imaging mass spectra plots </description> @@ -6,9 +6,9 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="2.2.1">r-gridextra</requirement> - <requirement type="package" version="2.2.1">r-ggplot2</requirement> - <requirement type="package" version="0.5.0">r-scales</requirement> + <requirement type="package" version="3.0">r-ggplot2</requirement> + <requirement type="package" version="2.3">r-gridextra</requirement> + <requirement type="package" version="1.0.0">r-scales</requirement> </expand> <command detect_errors="exit_code"> <![CDATA[ @@ -31,6 +31,7 @@ @DATA_PROPERTIES@ + ######################################## PDF ################################### ################################################################################ ################################################################################ @@ -51,7 +52,13 @@ ## set NA to 0 otherwise plot function will not work - spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero + ##spectra(msidata)[is.na(spectra(msidata)[])] = 0 ## in case of NA values they will be set to zero + + spectra_df = spectra(msidata)[] + spectra_df[is.na(spectra_df)] = 0 + print(paste0("Number of NA which were converted into 0:",sum(is.na(spectra_df)))) + spectra(msidata) = spectra_df + if (npeaks > 0){ @@ -88,7 +95,6 @@ ##################### IV) plot zoom-in mass spectrum ############### #if $chosenpixel.zoomedplot: - iData(msidata) <- iData(msidata)[] ## getting back data on disk #for $token in $chosenpixel.zoomedplot: @@ -253,6 +259,8 @@ print("Inputfile has no intensities > 0") dev.off() } + + ]]></configfile> </configfiles> <inputs>