| Previous changeset 9:1334cb4c6b68 (2019-11-30) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 46ae76d42d29ce02cf05b6ab735e0c305a86f9cd" |
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modified:
taxonomy_krona_chart.xml |
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added:
test-data/tax2.tax |
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removed:
test-data/krona_test1.html |
| b |
| 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 @@ -<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1"> +<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1+galaxy0"> <description>from taxonomic profile</description> <requirements> <requirement type="package" version="2.7.1">krona</requirement> @@ -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 ]]></command> @@ -79,7 +74,30 @@ <param name="max_rank" value="Genus"/> <param name="root_name" value="Root"/> <param name="combine_inputs" value="False"/> - <output name="output" file="krona_test1.html" ftype="html" lines_diff="102"/> + <output name="output" ftype="html"> + <assert_contents> + <has_text text="KRONA"/> + <has_text text="taxonomy_data"/> + <has_text text="Eukaryota"/> + <has_text text="Chordata"/> + <has_text text="Rodentia"/> + </assert_contents> + </output> + </test> + <test> + <param name="type_of_data_selector" value="taxonomy"/> + <param name="input" value="taxonomy_data.tax,tax2.tax" ftype="taxonomy" /> + <param name="max_rank" value="Genus"/> + <param name="root_name" value="Root"/> + <param name="combine_inputs" value="False"/> + <output name="output" ftype="html"> + <assert_contents> + <has_text text="KRONA"/> + <has_text text="taxonomy_data"/> + <has_text text="tax2"/> + <has_text text="Proteobacteria"/> + </assert_contents> + </output> </test> <test><!-- test with tabular inputs and multiple datasets --> <param name="type_of_data_selector" value="text"/> |
| b |
| 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 |
| b |
| b'@@ -1,6716 +0,0 @@\n-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\n-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\n- <head>\n- <meta charset="utf-8"/>\n- <link rel="shortcut icon" 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<rank><val>family</val></rank>\n- <count><val>94</val></count>\n- <node name="Murinae">\n- <rank><val>subfamily</val></rank>\n- <count><val>94</val></count>\n- <node name="Rattus">\n- <rank><val>genus</val></rank>\n- <count><val>94</val></count>\n- <members>\n- <vals><val>IA_1-296315</val><val>IA_1-322295</val></vals>\n- </members>\n- <unassigned><val>2</val></unassigned>\n- <node name="Rattus norvegicus">\n- <members>\n- <vals><val>IA_1-144417</val><val>IA_1-278966</val><val>IA_1-314709</val><val>IA_1-324951</val><val>IA_1-27817</val><val>IA_1-95255</val><val>IA_1-104173</val><val>IA_1-135979</val><val>IA_1-139090</val><val>IA_1-139090</val><val>IA_1-139090</val><val>IA_1-144996</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-160446</val><val>IA_1-161439</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-190855</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-205154</val><val>IA_1-216231</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-236286</val><val>IA_1-237681</val><val>IA_1-250166</val><val>IA_1-254274</val><val>IA_1-254274</val><val>IA_1-27817</val><val>IA_1-29000</val><val>IA_1-291427</val><val>IA_1-291427</val><val>IA_1-293054</val><val>IA_1-293054</val><val>IA_1-296315</val><val>IA_1-310974</val><val>IA_1-310974</val><val>IA_1-311282</val><val>IA_1-311282</val><val>IA_1-42600</val><val>IA_1-45102</val><val>IA_1-45102</val><val>IA_1-48105</val><val>IA_1-48105</val><val>IA_1-57254</val><val>IA_1-61975</val><val>IA_1-61975</val><val>IA_1-66943</val><val>IA_1-68288</val><val>IA_1-82334</val><val>IA_1-95526</val></vals>\n- </members>\n- <rank><val>species</val></rank>\n- <count><val>92</val></count>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- <node name="Bacteria">\n- <count><val>6</val></count>\n- <rank><val>superkingdom</val></rank>\n- <node name="Proteobacteria">\n- <count><val>6</val></count>\n- <rank><val>phylum</val></rank>\n- <node name="Gammaproteobacteria">\n- <rank><val>class</val></rank>\n- <count><val>6</val></count>\n- <node name="Enterobacteriales">\n- <rank><val>order</val></rank>\n- <count><val>6</val></count>\n- <node name="Enterobacteriaceae">\n- <rank><val>family</val></rank>\n- <count><val>6</val></count>\n- <node name="Shigella">\n- <count><val>6</val></count>\n- <rank><val>genus</val></rank>\n- <node name="Shigella flexneri">\n- <count><val>6</val></count>\n- <rank><val>species</val></rank>\n- <members>\n- <vals><val>IA_1-79371</val><val>IA_1-84488</val><val>IA_1-270826</val><val>IA_1-285361</val><val>IA_1-93958</val><val>IA_1-99821</val></vals>\n- </members>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n- </node>\n-</node>\n- </krona>\n-</div></body></html>\n' |
| b |
| 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 |
| b |
| @@ -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 |