Commit 7ab33d29 authored by khalid's avatar khalid
Browse files

Add signi. treshold to radsex tools

parent 924785ca
......@@ -21,7 +21,7 @@
outputs: [
{ name: eigenvectors, type: "txt", file: "*_eigenvects.txt", description: "Eigenvectors" },
{ name: eigenvalues, type: "txt", file: "*_eigenvals.txt", description: "Eigenvalues" },
{ name: varprop, type: "txt", file: "pca_varprop_mqc.txt", description: "variance proportion " },
{ name: varprop, type: "txt", file: "pca_varprop_mqc.txt", description: "variance proportion" },
{ name: pca_png, type: "png", file: "pca_topaxes_plot_mqc.png", description: "First 6 eigenvectors plots" },
{ name: axe1axe2_png, type: "png", file: "pca_axe1axe2_plot_mqc.png", description: "First 2 eigenvectors plots" },
],
......
......@@ -10,11 +10,14 @@ rule <step_name>__radsex_distrib:
params:
command = config["<step_name>__radsex_distrib_command"],
min_depth = config["<step_name>__radsex_min_depth"],
signif_threshold = config["<step_name>__radsex_signi_threshold"],
shell:
"{params.command} "+
"--markers-table {input.markers_table} "+
"--popmap {input.popmap_file} "+
"-o {output} "+
"-d {params.min_depth} "
"-d {params.min_depth} "+
"--signif-threshold {params.signif_threshold} "
#"--groups F,M"
\ No newline at end of file
......@@ -35,6 +35,16 @@
label: "Minimum depth to consider a marker present in an individual",
type: "numeric",
},
{
name: "radsex_signi_threshold",
prefix: "--signif-threshold",
value: 0.05,
min: 0,
max: 1,
step: 0.001,
label: "P-value threshold to consider a marker significantly associated with a phenotypic group",
type: "numeric",
},
],
},
],
......
......@@ -35,6 +35,16 @@
label: "Minimum depth to consider a marker present in an individual",
type: "numeric",
},
{
name: "radsex_signi_threshold",
prefix: "--signif-threshold",
value: 0.05,
min: 0,
max: 1,
step: 0.001,
label: "P-value threshold to consider a marker significantly associated with a phenotypic group",
type: "numeric",
},
],
},
],
......
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