Mercurial > repos > crs4 > taxonomy_krona_chart

comparison taxonomy_krona_chart.xml @ 8:c9f8fef1df74 draft

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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
comparison
equal deleted inserted replaced
7:73486cc6170e 8:c9f8fef1df74
1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1"> 1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1.1">
2 <description>from taxonomic profile</description> 2 <description>from taxonomic profile</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.6.1">krona</requirement> 4 <requirement type="package" version="2.6.1">krona</requirement>
5 </requirements> 5 </requirements>
6 <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command> 6 <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import re
9
8 #if $type_of_data.input[0].is_of_type('taxonomy'): 10 #if $type_of_data.input[0].is_of_type('taxonomy'):
9 ktImportGalaxy 11 ktImportGalaxy
10 -d '${type_of_data.max_rank}' 12 -d '${type_of_data.max_rank}'
11 -n '${root_name}' 13 -n '${root_name}'
12 -o '${output}' 14 -o '${output}'
17 #else: 19 #else:
18 ktImportText 20 ktImportText
19 -n '${root_name}' 21 -n '${root_name}'
20 -o '${output}' 22 -o '${output}'
21 ${combine_inputs} 23 ${combine_inputs}
22 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): 24 #for $input_dataset in $type_of_data.input:
23 '${input_dataset},${input_count}' 25 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
26 '${input_dataset},${identifier}'
24 #end for 27 #end for
25 #end if 28 #end if
26 && 29 &&
27 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi 30 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
28 ]]></command> 31 ]]></command>
76 <param name="max_rank" value="Genus"/> 79 <param name="max_rank" value="Genus"/>
77 <param name="root_name" value="Root"/> 80 <param name="root_name" value="Root"/>
78 <param name="combine_inputs" value="False"/> 81 <param name="combine_inputs" value="False"/>
79 <output name="output" file="krona_test1.html" ftype="html" lines_diff="102"/> 82 <output name="output" file="krona_test1.html" ftype="html" lines_diff="102"/>
80 </test> 83 </test>
84 <test><!-- test with tabular inputs and multiple datasets -->
85 <param name="type_of_data_selector" value="text"/>
86 <param name="input" value="pampa-small.tsv,anguil-small.tsv" ftype="tabular" />
87 <param name="max_rank" value="Genus"/>
88 <param name="root_name" value="Root"/>
89 <param name="combine_inputs" value="False"/>
90 <output name="output" ftype="html">
91 <assert_contents>
92 <has_text text="KRONA"/>
93 <has_text text="pampa-small"/>
94 <has_text text="anguil-small"/>
95 <has_text text="Proteobacteria"/>
96 </assert_contents>
97 </output>
98 </test>
81 </tests> 99 </tests>
82 <help> 100 <help>
83 **What it does** 101 **What it does**
84 102
85 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. 103 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_.