Mercurial > repos > crs4 > taxonomy_krona_chart
comparison taxonomy_krona_chart.xml @ 5:020b3087d0b7 draft
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 |
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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> |