# HG changeset patch # User iuc # Date 1608308172 0 # Node ID e9005d1f3cfd3357ab29b126adb38b04c62570ed # Parent 1334cb4c6b688368ddb7827b152b6fff416c1745 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 46ae76d42d29ce02cf05b6ab735e0c305a86f9cd" diff -r 1334cb4c6b68 -r e9005d1f3cfd taxonomy_krona_chart.xml --- a/taxonomy_krona_chart.xml Sat Nov 30 13:05:03 2019 -0500 +++ b/taxonomy_krona_chart.xml Fri Dec 18 16:16:12 2020 +0000 @@ -1,4 +1,4 @@ - + from taxonomic profile krona @@ -10,22 +10,17 @@ #if $type_of_data.input[0].is_of_type('taxonomy'): ktImportGalaxy -d '${type_of_data.max_rank}' - -n '${root_name}' - -o '${output}' - ${combine_inputs} - #for $input_count, $input_dataset in enumerate( $type_of_data.input ): - '${input_dataset},${input_count}' - #end for #else: ktImportText - -n '${root_name}' - -o '${output}' - ${combine_inputs} - #for $input_dataset in $type_of_data.input: - #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier)) - '${input_dataset},${identifier}' - #end for #end if + + -n '${root_name}' + -o '${output}' + ${combine_inputs} + #for $input_dataset in $type_of_data.input: + #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier)) + '${input_dataset},${identifier}' + #end for && if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi ]]> @@ -79,7 +74,30 @@ - + + + + + + + + + + + + + + + + + + + + + + + + diff -r 1334cb4c6b68 -r e9005d1f3cfd test-data/krona_test1.html --- a/test-data/krona_test1.html Sat Nov 30 13:05:03 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6716 +0,0 @@ - - - - - - - - - - - - - -

- - - members - count - unassigned - rank - - - 0 - - - 100 - - superkingdom - 94 - - kingdom - 94 - - phylum - 94 - - subphylum - 94 - - superclass - 94 - - class - 94 - - 94 - superorder - - 94 - order - - suborder - 94 - - family - 94 - - subfamily - 94 - - genus - 94 - - IA_1-296315IA_1-322295 - - 2 - - - IA_1-144417IA_1-278966IA_1-314709IA_1-324951IA_1-27817IA_1-95255IA_1-104173IA_1-135979IA_1-139090IA_1-139090IA_1-139090IA_1-144996IA_1-160446IA_1-160446IA_1-160446IA_1-160446IA_1-160446IA_1-160446IA_1-160446IA_1-160446IA_1-161439IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-190855IA_1-205154IA_1-205154IA_1-205154IA_1-205154IA_1-205154IA_1-205154IA_1-205154IA_1-205154IA_1-205154IA_1-205154IA_1-216231IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-236286IA_1-237681IA_1-250166IA_1-254274IA_1-254274IA_1-27817IA_1-29000IA_1-291427IA_1-291427IA_1-293054IA_1-293054IA_1-296315IA_1-310974IA_1-310974IA_1-311282IA_1-311282IA_1-42600IA_1-45102IA_1-45102IA_1-48105IA_1-48105IA_1-57254IA_1-61975IA_1-61975IA_1-66943IA_1-68288IA_1-82334IA_1-95526 - - species - 92 - - - - - - - - - - - - - - - 6 - superkingdom - - 6 - phylum - - class - 6 - - order - 6 - - family - 6 - - 6 - genus - - 6 - species - - IA_1-79371IA_1-84488IA_1-270826IA_1-285361IA_1-93958IA_1-99821 - - - - - - - - - - -

diff -r 1334cb4c6b68 -r e9005d1f3cfd test-data/tax2.tax --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tax2.tax Fri Dec 18 16:16:12 2020 +0000 @@ -0,0 +1,18 @@ +IA_1-79371 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604065 +IA_1-84488 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604065 +IA_1-270826 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-285361 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-93958 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-99821 591020 root Bacteria n n n Proteobacteria n n Gammaproteobacteria n n Enterobacteriales n n Enterobacteriaceae n n n Shigella n Shigella flexneri n 281604070 +IA_1-144417 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-278966 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-314709 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-324951 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604077 +IA_1-27817 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604153 +IA_1-95255 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604181 +IA_1-104173 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-135979 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-139090 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-139090 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-139090 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186 +IA_1-144996 10116 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Rodentia Sciurognathi n Muridae Murinae n n Rattus n Rattus norvegicus n 281604186