Galaxy |

xcms plot chromatogram tool metadata

Miscellaneous

Name: xcms plot chromatogram

Description: Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)

Id: xcms_plot_chromatogram

Guid: toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy1

Version: 3.12.0+galaxy1

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy1 (this tool)

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.6.1+galaxy2

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.6.1+galaxy1

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.6.1.0

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.4.4.0

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.4.3.0

toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.0.0.0

xcms_plot_chromatogram

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

bioconductor-xcms

3.12.0

package

r-batch

1.1_5

package

r-rcolorbrewer

1.1_2

package

unzip

6.0

package

Additional information about this tool

Command:

LC_ALL=C Rscript $__tool_directory__///xcms_plot_chromatogram.r

        images 'c("${"\",\"".join(map(str, $images))}")'

        #if str($sampleMetadata) != 'None':
            sampleMetadata '$sampleMetadata'
        #end if

        
        #if $file_load_section.file_load_conditional.file_load_select == "yes":
            #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
                #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
                #set singlefile_sampleName = '|'.join( [ str( $single_file.element_identifier ) for $single_file in $file_load_section.file_load_conditional.input ] )

                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
            #else
                zipfile '$file_load_section.file_load_conditional.input'
            #end if
        #end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

images: faahKO-single-class.xset.merged.group.retcor.RData
sampleMetadata: sampleMetadata.tab
file_load_section|file_load_conditional|input: ['wt15.CDF', 'ko16.CDF', 'ko15.CDF', 'wt16.CDF']
file_load_section|file_load_conditional|file_load_select: yes

name: value
name: value

faahKO-single-class.xset.merged.group.retcor.RData
sampleMetadata.tab
wt15.CDF
ko16.CDF
ko15.CDF
wt16.CDF
value