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Commit message:
planemo upload commit f03966304c7f36f2ff40f70665ff56663d3e640f |
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modified:
rgreat.R rgreat.xml |
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| diff -r 35c197ad8a80 -r d1107fb17398 rgreat.R --- a/rgreat.R Mon Nov 18 16:21:59 2024 +0000 +++ b/rgreat.R Tue Nov 19 13:03:37 2024 +0000 |
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| @@ -68,15 +68,13 @@ # Read the options from the default: commandArgs(TRUE) # Define option specification option_list <- list( - # Required options make_option("--input_regions", type = "character", help = "Input regions"), make_option("--input_hypo", type = "character", help = "Input hypo"), make_option("--input_hyper", type = "character", help = "Input hyper"), make_option("--output_hypo", type = "character", help = "Output hypo"), make_option("--output_hyper", type = "character", help = "Output hyper"), make_option("--biomart_dataset", type = "character", help = "Biomart dataset"), - - # Optional options + make_option("--cytosine_context", type = "character", help = "Cytosine context"), make_option("--min_gene_set_size", type = "integer", default = NULL, help = "Minimum gene set size [optional]"), make_option("--mode", type = "character", default = NULL, help = "Mode [optional]"), make_option("--basal_upstream", type = "integer", default = NULL, help = "Basal upstream [optional]"), |
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| diff -r 35c197ad8a80 -r d1107fb17398 rgreat.xml --- a/rgreat.xml Mon Nov 18 16:21:59 2024 +0000 +++ b/rgreat.xml Tue Nov 19 13:03:37 2024 +0000 |
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| @@ -33,6 +33,7 @@ --output_hypo '$output_hypo' --output_hyper '$output_hyper' --biomart_dataset '$biomart_dataset' + --cytosine_context '$cytosine_context' #if $advanced_parameters.advanced_options --min_gene_set_size $advanced_parameters.min_gene_set_size --mode $advanced_parameters.gene_extension_mode.mode @@ -133,7 +134,23 @@ </test> </tests> <help><![CDATA[ - scream for help + GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This tools implements the GREAT algorithm (the local GREAT analysis). rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions. + + min_gene_set_size: Minimal size of gene sets. + + mode: The mode to extend genes. Value should be one of 'basalPlusExt', 'twoClosest' and 'oneClosest'. + + extend_from: Should the gene be extended only from its TSS or the complete gene? + + basal_upstream: In 'basalPlusExt' mode, number of base pairs extending to the upstream of TSS to form the basal domains. + + basal_downstream: In 'basalPlusExt' mode, number of base pairs extending to the downstream of TSS to form the basal domains. + + extension: Extensions from the basal domains. + + background: Background regions. The value can also be a vector of chromosome names. + + exclude: Regions that are excluded from analysis such as gap regions (which can be get by getGapFromUCSC). The value can also be a vector of chromosome names. It also allows a special character value "gap" so that gap regions for corresponding organism will be removed from the analysis. ]]></help> <citations> |