Mercurial > repos > iuc > funannotate_compare
diff funannotate_compare.xml @ 12:37f9a80ca41e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
author | iuc |
---|---|
date | Fri, 07 Mar 2025 22:36:43 +0000 |
parents | 57c6718cbfcc |
children |
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--- a/funannotate_compare.xml Wed Jun 26 09:38:43 2024 +0000 +++ b/funannotate_compare.xml Fri Mar 07 22:36:43 2025 +0000 @@ -9,6 +9,13 @@ </requirements> <version_command>funannotate check --show-versions</version_command> <command><![CDATA[ +## Needed by some subprocess invoked internally +## https://github.com/nextgenusfs/funannotate/issues/905 +export FUNANNOTATE_DB='$database.fields.path' && + +## show detailed info about the reference DB on stdout +funannotate database && + #set $inputs = "" #for i, f in enumerate($input): #set $inputs = $inputs + " input" + str($i) + ".gbk" @@ -28,7 +35,9 @@ --run_dnds ${run_dnds} #end if -## need to add --outgroup option some day (hard to get an up to date/customizable list) +#if $outgroup + --outgroup '$outgroup' +#end if --go_fdr ${go_fdr} @@ -62,7 +71,7 @@ <column name="value" index="0" /> <column name="name" index="1" /> <column name="path" index="3" /> - <filter type="sort_by" column="0" /> + <filter type="sort_by" column="0" reverse_sort_order="true"/> <filter type="static_value" column="2" value="1.0" /> </options> </param> @@ -76,6 +85,14 @@ <param argument="--go_fdr" type="float" value="0.05" label="P-value for FDR GO-enrichment" /> <param argument="--heatmap_stdev" type="float" value="1.0" label="Cut-off for heatmap" /> <param argument="--num_orthos" type="integer" value="500" label="Number of Single-copy orthologs to use for ML" /> + <param argument="--outgroup" type="select" optional="true" label="Outgroup species" help="Name of species to use for ML outgroup. Default: no outgroup"> + <options from_data_table="funannotate_options"> + <column name="value" index="0" /> + <column name="name" index="1" /> + <filter type="static_value" column="2" value="outgroup"/> + <filter type="param_value" column="3" ref="database"/> + </options> + </param> <param argument="--proteinortho" type="data" format="tabular" optional="true" label="Proteinortho POFF results" help="TSV format, if available"/> <conditional name="ml"> @@ -122,6 +139,7 @@ <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" /> <param name="database" value="2021-07-20-120000" /> <param name="run_dnds" value="full" /> + <param name="outgroup" value="botrytis_cinerea.dikarya"/> <conditional name="ml"> <param name="ml_method" value="raxml" /> </conditional>