Repository revision
17:80600735685d

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

MSI mz images tool metadata
Miscellaneous
mass spectrometry imaging m/z heatmaps
cardinal_mz_images
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/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_mz_images/cardinal_mz_images/2.10.0.0 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.2
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.6.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/2.4.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.0
cardinal_mz_images
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-cardinal 2.10.0 package
r-gridextra 2.3 package
Functional tests
name inputs outputs required files
Test-1 infile:
filename: Testfile_imzml
calibrant_file: inputpeptides.tabular
mz_column: 1
name_column: 2
plusminus_dalton: 0.25
image_contrast: histogram
colorkey: True
name: value

inputpeptides.tabular
value
Test-2 infile:
filename: Testfile_analyze75
calibrant_file: inputpeptides2.tabular
mz_column: 1
name_column: 1
plusminus_dalton: 0.5
image_smoothing: gaussian
colorscale: magma
colorkey: True
svg_pixelimage: True
name: value
name: value

inputpeptides2.tabular
value
Test-3 infile: preprocessed.RData
filename: Testfile_rdata
calibrant_file: inputpeptides.tabular
mz_column: 1
name_column: 2
plusminus_dalton: 0.5
colorkey: True
name: value
preprocessed.RData
inputpeptides.tabular
value
Test-4 infile: empty_spectra.rdata
filename: Testfile_rdata
calibrant_file: inputpeptides2.tabular
mz_column: 1
name_column: 1
plusminus_dalton: 0.5
colorscale: plasma
colorkey: False
name: value
empty_spectra.rdata
inputpeptides2.tabular
value
Test-5 infile:
processed_cond|accuracy: 200
processed_cond|units: ppm
processed_cond|processed_file: processed
calibrant_file: inputpeptides.tabular
mz_column: 1
name_column: 2
light_mode: black
overlay_cond|colours_0|feature_color: #ff00ff
overlay_cond|colours_1|feature_color: #1f497d
overlay_cond|colours_2|feature_color: #00b050
overlay_cond|legend_position: topleft
overlay_cond|overlay_selection: yes_overlay
name: value

inputpeptides.tabular
value