# HG changeset patch # User jjohnson # Date 1495813510 14400 # Node ID b3ae16ffb54eaf981e722e12581e6859b1b1605b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper diff -r 000000000000 -r b3ae16ffb54e eggnog_mapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eggnog_mapper.xml Fri May 26 11:45:10 2017 -0400 @@ -0,0 +1,364 @@ + + functional sequence annotation by orthology + + eggnog-mapper + + + + + python emapper.py --version + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. + Queries not having a significant seed orthologs will not be annotated. + + + + + Min bit score expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. + Queries not having a significant seed orthologs will not be annotated. Default=60 + + +
+
+ + + +
+
+ + + + + + + + output_options['no_annot'] == '' + + + + + + db['mode'] == 'hmmer' + + + + + + output_options['report_orthologs'] + + + + + + hits. 4 + fields required: query, hit, evalue, score. Implies + --no_search and --no_refine. + + ]]> + + 10.1093/nar/gkv1248 + +
diff -r 000000000000 -r b3ae16ffb54e tool-data/eggnog_mapper.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper.loc.sample Fri May 26 11:45:10 2017 -0400 @@ -0,0 +1,9 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +#name value type data_dir +#eggnog_4.5 eggnog_4.5 data /depot/data2/galaxy/eggnog/eggnog_4.5/data +#eggnog_4.5arcNOG arcNOG hmmer /depot/data2/galaxy/eggnog/eggnog_4.5/data +#eggnog_4.5euk euk hmmer /depot/data2/galaxy/eggnog/eggnog_4.5/data +#eggnog_4.5dmnd eggnog_proteins.dmnd diamond /depot/data2/galaxy/eggnog/eggnog_4.5/data +# diff -r 000000000000 -r b3ae16ffb54e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri May 26 11:45:10 2017 -0400 @@ -0,0 +1,7 @@ + + + + name,value,type,data_dir + +
+