Repository revision
6:82f6c2f4332d

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

MSI segmentation tool metadata
Miscellaneous
mass spectrometry imaging spatial clustering
cardinal_segmentations
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3
1.12.1.3
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/2.4.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.3 (this tool)
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.2
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.0
cardinal_segmentations
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-cardinal 1.12.1 package
r-base 3.5.1 package
r-gridextra 2.3 package
r-lattice 0.20_35 package
Functional tests
name inputs outputs required files
Test-1 image_type: False
colours_1|feature_color: #0000FF
colours_0|feature_color: #ff00ff
infile:
segm_cond|segmentationtool: pca
attributes: name
attributes: name
attributes: name

name
Test-2 output_rdata: True
segm_cond|kmeans_toplabels: 20
segm_cond|kmeans_k: 2,3
segm_cond|segmentationtool: kmeans
colours_1|feature_color: #0000FF
segm_cond|kmeans_r: 1:3
colours_2|feature_color: #00C957
colours_0|feature_color: #ff00ff
infile:
attributes: name
attributes: name
attributes: name
attributes: name

name
Test-3 segm_cond|centroids_r: 1,2
colours_4|feature_color: #848484
colours_3|feature_color: #FFD700
colours_1|feature_color: #00C957
segm_cond|centroids_k: 3
segm_cond|centroids_toplabels: 50
colours_2|feature_color: #B0171F
segm_cond|segmentationtool: centroids
colours_0|feature_color: #0000FF
infile: preprocessed.RData
attributes: name
attributes: name
attributes: name
preprocessed.RData
name