comparison xcms_plot_eic.xml @ 1:cbedca3ba6e1 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit bb7574b871cff739f7abbda62a5269ec1f98971f

0:51015f22fcb7

    <configfiles>
        <configfile name="plot_eic">
library(xcms)
library(MsExperiment)
library(Spectra)
mse = readMsExperiment(file.path('${input}'))
offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel})
png(filename = '${output_filename}')
plot(chr)
dev.off()
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="base_params"/>
        <param type="integer" value="1" name="mslevel" min="1" label="MS Level" help="MS level for the EIC"/>
    </inputs>
    <outputs>
        <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier"  />
    </outputs>
    <tests>

1:cbedca3ba6e1

    <configfiles>
        <configfile name="plot_eic">
library(xcms)
library(MsExperiment)
library(Spectra)

sessionInfo()

mse = readMsExperiment(file.path('${input}'))
offset = ${tolerance_ppm} * 1e-6 * ${mz_value}
chr = chromatogram(mse, mz = ${mz_value} + c(-offset, offset), msLevel = ${mslevel})
png(filename = '${output_filename}')
plot(chr)
dev.off()
        </configfile>
    </configfiles>
    <inputs>
        <expand macro="base_params"/>
    </inputs>
    <outputs>
        <data name="output_filename" format="png" label="EIC plot at m/z=$mz_value of $input.element_identifier"  />
    </outputs>
    <tests>