| Previous changeset 0:3700c6ff0eee (2024-11-07) Next changeset 2:13266dc1841c (2024-11-08) |
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Commit message:
planemo upload commit 20b328b897e189e3ece16bb42fc46cfd5ec25ec2 |
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modified:
rgreat.xml |
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| diff -r 3700c6ff0eee -r 1bb5501a3292 rgreat.xml --- a/rgreat.xml Thu Nov 07 14:24:33 2024 +0000 +++ b/rgreat.xml Fri Nov 08 10:29:20 2024 +0000 |
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| @@ -59,12 +59,16 @@ <expand macro="biomart" /> </param> --> - <param name="biomart_dataset" type="select" data_table="biomart_datasets" label="Select organism and dataset" help="Choose the organism and corresponding dataset from BioMartGOGeneSets"> + <param name="biomart_dataset" type="select" label="Select organism and dataset" help="Choose the organism and corresponding dataset from BioMartGOGeneSets"> + <options from_data_table="biomart_datasets" /> + </param> <conditional name="advanced_parameters"> - <param name="advanced_options" type="boolean" label="Show advanced options?" help="Check this box to set additional advanced parameters." checked="false" /> + <param name="advanced_options" type="select" value="false" label="Show advanced options?" help="Check this box to set additional advanced parameters."> + <option value="false">No</option> + <option value="true">Yes</option> + </param> <when value="true"> <param name="min_gene_set_size" type="integer" value="10" min="1" label="Minimal size of gene sets" help="Minimal size of gene sets to be considered in the analysis." /> - <conditional name="gene_extension_mode"> <param name="mode" type="select" label="Mode to extend genes"> <option value="basalPlusExt">Basal Plus Extension</option> @@ -78,14 +82,11 @@ <when value="twoClosest" /> <when value="oneClosest" /> </conditional> - <param name="extend_from" type="select" label="Extend gene from"> <option value="tss">TSS only</option> <option value="complete">Complete gene</option> </param> - - <param name="extension" type="integer" value="1000000" min="0" label="Extension from basal domains" help="Extensions from the basal domains." /> - + <param name="extension" type="integer" value="1000000" min="0" label="Extension from basal domains" help="Extensions from the basal domains." /> <param name="exclude" type="text" area="true" optional="true" label="Excluded regions" help="Regions that are excluded from analysis such as gap regions. The value can also be a vector of chromosome names. Use 'gap' to remove gap regions for the corresponding organism." > <validator type="regex" message="Use 'gap' or provide a list of chromosome names"> ^(gap|(\w+,?\s*)+)$ @@ -94,7 +95,6 @@ </when> <when value="false" /> </conditional> - </inputs> <outputs> <data name="output_hypo" format="rds" label="Output hypo-methyla: ${cytosine_context} context" /> |