Repository revision
17:a7fb9b395ddf

Repository 'cardinal_quality_report'
hg clone https://toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report

MSI Qualitycontrol tool metadata
Miscellaneous
mass spectrometry imaging QC
cardinal_quality_report
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.10.0.0
2.10.0.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.10.0.0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.6.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.4.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/2.4.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.4
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.3
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.0
cardinal_quality_report
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-cardinal 2.10.0 package
r-gridextra 2.3 package
r-ggplot2 3.3.5 package
r-rcolorbrewer 1.1_2 package
r-kernsmooth 2.23_20 package
r-scales 1.1.1 package
r-pheatmap 1.0.12 package
Additional information about this tool
#if $infile.ext == 'imzml'
            ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
            ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
        #elif $infile.ext == 'analyze75'
            ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
            ln -s '${infile.extra_files_path}/img' infile.img &&
            ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
        #else
            ln -s $infile infile.RData &&
        #end if
    
        cat '${cardinal_qualitycontrol_script}' &&
        Rscript '${cardinal_qualitycontrol_script}'
    
    
None
False
Functional tests
name inputs outputs required files
Test-1 infile:
processed_cond|accuracy: 400
processed_cond|units: ppm
processed_cond|processed_file: processed
tabular_annotation|load_annotation: no_annotation
filename: Testfile_imzml
calibrant_file: inputcalibrantfile1.tabular
mz_column: 1
name_column: 1
plusminus_ppm: 100
do_pca: True
calibrantratio_0|mass1: 328.9
calibrantratio_0|mass2: 398.8
calibrantratio_0|distance: 500
calibrantratio_0|filenameratioplot: Ratio of mz 328.9 and mz 398.8
name: value

inputcalibrantfile1.tabular
value
Test-2 infile:
tabular_annotation|load_annotation: no_annotation
filename: Testfile_analyze75
do_pca: True
name: value

value
Test-3 infile: 3_files_combined.RData
tabular_annotation|annotation_file: annotations_rdata.tabular
tabular_annotation|column_x: 1
tabular_annotation|column_y: 2
tabular_annotation|column_names: 3
tabular_annotation|tabular_header: True
tabular_annotation|load_annotation: yes_annotation
filename: Testfile_rdata
calibrant_file: inputcalibrantfile1.tabular
mz_column: 1
name_column: 1
plusminus_ppm: 100
do_pca: True
name: value
3_files_combined.RData
annotations_rdata.tabular
inputcalibrantfile1.tabular
value
Test-4 infile: empty_spectra.rdata
tabular_annotation|load_annotation: no_annotation
filename: Testfile_rdata
calibrant_file: inputcalibrantfile2.txt
mz_column: 1
name_column: 2
do_pca: False
name: value
empty_spectra.rdata
inputcalibrantfile2.txt
value
Test-5 infile:
processed_cond|accuracy: 200
processed_cond|units: ppm
processed_cond|processed_file: processed
tabular_annotation|load_annotation: no_annotation
calibrant_file: inputcalibrantfile1.tabular
mz_column: 1
name_column: 1
report_depth: False
name: value

inputcalibrantfile1.tabular
value