Mercurial > repos > crs4 > taxonomy_krona_chart
changeset 8:c9f8fef1df74 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 67d6ebc478c0cb5b7923de3f60f889a9b56f0856
| author | iuc |
|---|---|
| date | Fri, 13 Apr 2018 15:32:04 -0400 |
| parents | 73486cc6170e |
| children | 1334cb4c6b68 |
| files | taxonomy_krona_chart.xml test-data/anguil-small.tsv test-data/pampa-small.tsv |
| diffstat | 3 files changed, 421 insertions(+), 3 deletions(-) [+] |
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--- a/taxonomy_krona_chart.xml Mon Feb 19 06:29:08 2018 -0500 +++ b/taxonomy_krona_chart.xml Fri Apr 13 15:32:04 2018 -0400 @@ -1,10 +1,12 @@ -<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1"> +<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1.1"> <description>from taxonomic profile</description> <requirements> <requirement type="package" version="2.6.1">krona</requirement> </requirements> <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command> <command detect_errors="exit_code"><![CDATA[ + #import re + #if $type_of_data.input[0].is_of_type('taxonomy'): ktImportGalaxy -d '${type_of_data.max_rank}' @@ -19,8 +21,9 @@ -n '${root_name}' -o '${output}' ${combine_inputs} - #for $input_count, $input_dataset in enumerate( $type_of_data.input ): - '${input_dataset},${input_count}' + #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 && @@ -78,6 +81,21 @@ <param name="combine_inputs" value="False"/> <output name="output" file="krona_test1.html" ftype="html" lines_diff="102"/> </test> + <test><!-- test with tabular inputs and multiple datasets --> + <param name="type_of_data_selector" value="text"/> + <param name="input" value="pampa-small.tsv,anguil-small.tsv" ftype="tabular" /> + <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="pampa-small"/> + <has_text text="anguil-small"/> + <has_text text="Proteobacteria"/> + </assert_contents> + </output> + </test> </tests> <help> **What it does**
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/anguil-small.tsv Fri Apr 13 15:32:04 2018 -0400 @@ -0,0 +1,200 @@ +249 Bacteria(100) Verrucomicrobia(100) Spartobacteria(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) +145 Bacteria(100) Proteobacteria(100) Alphaproteobacteria(100) Rhizobiales(100) Bradyrhizobiaceae(100) Bradyrhizobiaceae_unclassified(70) +156 Bacteria(100) Acidobacteria(100) Acidobacteria_Gp4(100) Gp4(100) Gp4_unclassified(100) Gp4_unclassified(100) +184 Bacteria(100) Verrucomicrobia(100) Spartobacteria(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) +108 Bacteria(100) Bacteria_unclassified(100) Bacteria_unclassified(100) Bacteria_unclassified(100) Bacteria_unclassified(100) Bacteria_unclassified(100) +107 Bacteria(100) Acidobacteria(100) Acidobacteria_Gp6(100) Gp6(100) Gp6_unclassified(100) Gp6_unclassified(100) +94 Bacteria(100) 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pampa-small.tsv Fri Apr 13 15:32:04 2018 -0400 @@ -0,0 +1,200 @@ +680 Bacteria(100) Verrucomicrobia(100) Spartobacteria(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) +132 Bacteria(100) Proteobacteria(100) Alphaproteobacteria(100) Rhizobiales(100) Bradyrhizobiaceae(100) Bradyrhizobiaceae_unclassified(75) +72 Bacteria(100) Acidobacteria(100) Acidobacteria_Gp4(100) Gp4(100) Gp4_unclassified(100) Gp4_unclassified(100) +30 Bacteria(100) Verrucomicrobia(100) Spartobacteria(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) Spartobacteria_unclassified(100) +67 Bacteria(100) Bacteria_unclassified(100) Bacteria_unclassified(100) Bacteria_unclassified(100) Bacteria_unclassified(100) Bacteria_unclassified(100) +51 Bacteria(100) Acidobacteria(100) Acidobacteria_Gp6(100) Gp6(100) Gp6_unclassified(100) Gp6_unclassified(100) +47 Bacteria(100) Acidobacteria(100) 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