Repository revision
9:b83fbc90161e

Repository 'raceid_filtnormconf'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf

Initial processing using RaceID tool metadata
Miscellaneous
Initial processing using RaceID
performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data
raceid_filtnormconf
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy3
0.2.3+galaxy3
Rscript '$__tool_directory__/scripts/cluster.R' 2>&1 | head -1 | cut -d' ' -f 2
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy3 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/0.2.3+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.1
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.0.2.3
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.0.2.2
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.0.2.1
raceid_filtnormconf
Requirements (dependencies defined in the <requirements> tag set)
name version type
r-raceid 0.2.3 package
Additional information about this tool
Rscript '$__tool_directory__/scripts/cluster.R' '$userconf' 2> '$outlog' > /dev/null
None
False
Functional tests
name inputs outputs required files
Test-1 intable: use.intestinal
 name: value
name: value
name: value
 use.intestinal
value
Test-2 intable: matrix.tabular
filt|mintotal: 1050
filt|minexpr: 1
filt|minnumber: 3
 name: value
name: value
 matrix.tabular
value
Test-3 intable: use.intestinal
filt|mintotal: 3000
filt|minexpr: 5
filt|minnumber: 5
filt|use|knn: 10
filt|use|ccor: 0.4
filt|use|bmode: RaceID
filt|use|def: no
 name: value
 use.intestinal
value
Test-4 intable: use.intestinal
filt|hist_geq_one: True
 name: value
 use.intestinal
value
Test-5 intable: use.intestinal
filt|mintotal: 2000
filt|minexpr: 3
filt|minnumber: 2
filt|use|knn: 5
filt|use|CGenes: Gga3,Ggact,Ggct
filt|use|FGenes: Zxdc,Zyg11a,Zyg11b,Zyx
filt|use|LBatch_regexes: ^I5,^II5,^III5,^IV5d,^V5d
filt|use|ccor: 0.5
filt|use|ccc|pvalue: 0.05
filt|use|ccc|quant: 0.05
filt|use|ccc|ncomp: 3
filt|use|ccc|dimr: True
filt|use|ccc|mode: pca
filt|use|ccc|logscale: True
filt|use|ccc|use: yes
filt|use|def: no
 name: value
 use.intestinal
value