Repository revision
1:b24e4f6c8b4d

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

CheckM plot tool metadata
Miscellaneous
CheckM plot
for assessing the quality of genome bins
checkm_plot
toolshed.g2.bx.psu.edu/repos/iuc/checkm_plot/checkm_plot/1.2.0+galaxy0
1.2.0+galaxy0
checkm
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/checkm_plot/checkm_plot/1.2.3+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/checkm_plot/checkm_plot/1.2.0+galaxy0 (this tool)
checkm_plot
Requirements (dependencies defined in the <requirements> tag set)
name version type
checkm-genome 1.2.0 package
samtools 1.15.1 package
Functional tests
name inputs outputs required files
Test-1 bins|bins_coll: list collection
bins|select: collection
plot|dist_value: 100
plot|gc_window_size: 5000
plot|gc_bin_width: 0.01
plot|command: gc_plot
image_type: eps
dpi: 600
font_size: 8
width: 6.5
height: 3.5
637000110.fna
Test-2 bins|bins_coll: list collection
bins|select: collection
plot|gff: list collection
plot|dist_value: 100
plot|cd_window_size: 10000
plot|cd_bin_width: 0.01
plot|command: coding_plot
image_type: png
dpi: 600
font_size: 8
width: 6.5
height: 3.5
637000110.fna
637000110.gff
Test-3 bins|bins_coll: list collection
bins|select: collection
plot|gff: list collection
plot|tetra_profile: tetra
plot|dist_value: 100
plot|td_window_size: 5000
plot|td_bin_width: 0.01
plot|command: tetra_plot
image_type: pdf
dpi: 600
font_size: 8
width: 6.5
height: 3.5
637000110.fna
637000110.gff
tetra
Test-4 bins|bins_coll: list collection
bins|select: collection
plot|gff: list collection
plot|tetra_profile: tetra
plot|dist_value: 100
plot|gc_window_size: 5000
plot|gc_bin_width: 0.01
plot|cd_window_size: 10000
plot|cd_bin_width: 0.01
plot|td_window_size: 5000
plot|td_bin_width: 0.01
plot|command: dist_plot
image_type: png
dpi: 600
font_size: 8
width: 6.5
height: 3.5
637000110.fna
637000110.gff
tetra
Test-5 bins|bins_coll: list collection
bins|select: collection
plot|step_size: 0.05
plot|command: nx_plot
image_type: ps
dpi: 600
font_size: 8
width: 6.5
height: 3.5
637000110.fna
Test-6 bins|bins_coll: list collection
bins|select: collection
plot|fig_padding: 0.2
plot|command: len_hist
image_type: svg
dpi: 600
font_size: 8
width: 6.5
height: 3.5
637000110.fna
Test-7 bins|bins_coll: list collection
bins|select: collection
plot|genes_fna: list collection
plot|marker_gene_stats: marker_gene_stats.tsv
plot|bin_stats_ext: bin_stats_ext.tsv
plot|fig_padding: 0.2
plot|command: marker_plot
image_type: png
dpi: 600
font_size: 8
width: 6.5
height: 3.5
637000110.fna
637000110.faa
marker_gene_stats.tsv
bin_stats_ext.tsv