Mercurial > repos > crs4 > taxonomy_krona_chart

comparison taxonomy_krona_chart.xml @ 5:020b3087d0b7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 664ef05c64e91acc8355256d59e5c8e4f779ece9
author iuc
date Fri, 05 May 2017 11:15:46 -0400
parents 8e2be617b437
children d41b98e72c4c
comparison
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4:8e2be617b437 5:020b3087d0b7
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><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $type_of_data.input[0].is_of_type('taxonomy'): 8 #if $type_of_data.input[0].is_of_type('taxonomy'):
9 ktImportGalaxy 9 ktImportGalaxy
10 -d '${type_of_data.max_rank}' 10 -d '${type_of_data.max_rank}'
11 -n '${root_name}' 11 -n '${root_name}'
12 -o '${output}' 12 -o '${output}'
21 ${combine_inputs} 21 ${combine_inputs}
22 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): 22 #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
23 '${input_dataset},${input_count}' 23 '${input_dataset},${input_count}'
24 #end for 24 #end for
25 #end if 25 #end if
26 && [ -d '${output}.files' ] && ( mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}/' ) 26 &&
27 if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
27 ]]></command> 28 ]]></command>
28 <inputs> 29 <inputs>
29 <conditional name="type_of_data"> 30 <conditional name="type_of_data">
30 <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text"> 31 <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text">
31 <option value="taxonomy" selected="True">Taxonomy</option> 32 <option value="taxonomy" selected="True">Taxonomy</option>