Mercurial > repos > crs4 > taxonomy_krona_chart

comparison taxonomy_krona_chart.xml @ 10:e9005d1f3cfd draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 46ae76d42d29ce02cf05b6ab735e0c305a86f9cd"
author iuc
date Fri, 18 Dec 2020 16:16:12 +0000
parents 1334cb4c6b68
children
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9:1334cb4c6b68 10:e9005d1f3cfd
1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1"> 1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.7.1+galaxy0">
2 <description>from taxonomic profile</description> 2 <description>from taxonomic profile</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7.1">krona</requirement> 4 <requirement type="package" version="2.7.1">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>
8 #import re 8 #import re
9 9
10 #if $type_of_data.input[0].is_of_type('taxonomy'): 10 #if $type_of_data.input[0].is_of_type('taxonomy'):
11 ktImportGalaxy 11 ktImportGalaxy
12 -d '${type_of_data.max_rank}' 12 -d '${type_of_data.max_rank}'
13 -n '${root_name}'
14 -o '${output}'
15 ${combine_inputs}
16 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
17 '${input_dataset},${input_count}'
18 #end for
19 #else: 13 #else:
20 ktImportText 14 ktImportText
21 -n '${root_name}'
22 -o '${output}'
23 ${combine_inputs}
24 #for $input_dataset in $type_of_data.input:
25 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
26 '${input_dataset},${identifier}'
27 #end for
28 #end if 15 #end if
16
17 -n '${root_name}'
18 -o '${output}'
19 ${combine_inputs}
20 #for $input_dataset in $type_of_data.input:
21 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
22 '${input_dataset},${identifier}'
23 #end for
29 && 24 &&
30 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi 25 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
31 ]]></command> 26 ]]></command>
32 <inputs> 27 <inputs>
33 <conditional name="type_of_data"> 28 <conditional name="type_of_data">
77 <param name="type_of_data_selector" value="taxonomy"/> 72 <param name="type_of_data_selector" value="taxonomy"/>
78 <param name="input" value="taxonomy_data.tax" ftype="taxonomy" /> 73 <param name="input" value="taxonomy_data.tax" ftype="taxonomy" />
79 <param name="max_rank" value="Genus"/> 74 <param name="max_rank" value="Genus"/>
80 <param name="root_name" value="Root"/> 75 <param name="root_name" value="Root"/>
81 <param name="combine_inputs" value="False"/> 76 <param name="combine_inputs" value="False"/>
82 <output name="output" file="krona_test1.html" ftype="html" lines_diff="102"/> 77 <output name="output" ftype="html">
78 <assert_contents>
79 <has_text text="KRONA"/>
80 <has_text text="taxonomy_data"/>
81 <has_text text="Eukaryota"/>
82 <has_text text="Chordata"/>
83 <has_text text="Rodentia"/>
84 </assert_contents>
85 </output>
86 </test>
87 <test>
88 <param name="type_of_data_selector" value="taxonomy"/>
89 <param name="input" value="taxonomy_data.tax,tax2.tax" ftype="taxonomy" />
90 <param name="max_rank" value="Genus"/>
91 <param name="root_name" value="Root"/>
92 <param name="combine_inputs" value="False"/>
93 <output name="output" ftype="html">
94 <assert_contents>
95 <has_text text="KRONA"/>
96 <has_text text="taxonomy_data"/>
97 <has_text text="tax2"/>
98 <has_text text="Proteobacteria"/>
99 </assert_contents>
100 </output>
83 </test> 101 </test>
84 <test><!-- test with tabular inputs and multiple datasets --> 102 <test><!-- test with tabular inputs and multiple datasets -->
85 <param name="type_of_data_selector" value="text"/> 103 <param name="type_of_data_selector" value="text"/>
86 <param name="input" value="pampa-small.tsv,anguil-small.tsv" ftype="tabular" /> 104 <param name="input" value="pampa-small.tsv,anguil-small.tsv" ftype="tabular" />
87 <param name="max_rank" value="Genus"/> 105 <param name="max_rank" value="Genus"/>