| Previous changeset 3:f11a04ed443b (2016-03-29) Next changeset 5:020b3087d0b7 (2017-05-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit d62a0a2d4d0a8ac23014f09c1958d7ca0ea4fbb6 |
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modified:
taxonomy_krona_chart.xml |
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removed:
tool_dependencies.xml |
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| diff -r f11a04ed443b -r 8e2be617b437 taxonomy_krona_chart.xml --- a/taxonomy_krona_chart.xml Tue Mar 29 08:53:26 2016 -0400 +++ b/taxonomy_krona_chart.xml Thu May 04 06:04:23 2017 -0400 |
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| @@ -1,39 +1,30 @@ -<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.0"> +<tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1"> <description>from taxonomic profile</description> <requirements> - <requirement type="package" version="2.6">krona</requirement> + <requirement type="package" version="2.6.1">krona</requirement> </requirements> <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command> - <command> - <![CDATA[ - - #if $type_of_data.input[0].is_of_type('taxonomy'): - + <command><![CDATA[ + #if $type_of_data.input[0].is_of_type('taxonomy'): ktImportGalaxy - -d "${type_of_data.max_rank}" - -n "${root_name}" - -o "${output}" + -d '${type_of_data.max_rank}' + -n '${root_name}' + -o '${output}' ${combine_inputs} #for $input_count, $input_dataset in enumerate( $type_of_data.input ): - "${input_dataset},${input_count}" + '${input_dataset},${input_count}' #end for - - #else: - + #else: ktImportText - -n "${root_name}" - -o "${output}" + -n '${root_name}' + -o '${output}' ${combine_inputs} #for $input_count, $input_dataset in enumerate( $type_of_data.input ): - "${input_dataset},${input_count}" + '${input_dataset},${input_count}' #end for - - #end if - -&& [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" ) - ]]> - - </command> + #end if + && [ -d '${output}.files' ] && ( mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}/' ) + ]]></command> <inputs> <conditional name="type_of_data"> <param name="type_of_data_selector" type="select" label="What is the type of your input data" help="Select between Galaxy Taxonomy and MetaPhlAn Text"> @@ -43,7 +34,7 @@ <when value="taxonomy"> <param name="input" type="data" format="taxonomy" multiple="True" label="Input file" help="Select a taxonomy dataset" /> <param name="max_rank" type="select" label="show ranks from root to" help="-d; Show all level from root up to this point"> - <option value="8">Class</option> + <option value="8">Class</option> <option value="0">Show entire tree</option> <option value="1">Superkingdom</option> <option value="2">Kingdom</option> @@ -72,7 +63,7 @@ </when> </conditional> <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called "Root""/> - <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/> + <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" checked="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/> </inputs> <outputs> <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/> @@ -90,7 +81,7 @@ <help> **What it does** -This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. +This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. .. _Krona: https://github.com/marbl/Krona/wiki @@ -100,7 +91,7 @@ **Krona options** The Galaxy version supports the following options:: - + -n Name of the highest level. -c Combine data from each file, rather than creating separate datasets within the chart. -d Maximum depth of wedges to include in the chart. @@ -112,13 +103,11 @@ This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ -.. _MIT license: http://opensource.org/licenses/MIT +.. _MIT license: https://opensource.org/licenses/MIT You can use this tool only if you agree to the license terms of: `Krona`_. -.. _Krona: http://sourceforge.net/p/krona/home/krona/ - - +.. _Krona: https://github.com/marbl/Krona/wiki </help> <citations> <citation type="doi">10.1186/1471-2105-12-385</citation> |
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| diff -r f11a04ed443b -r 8e2be617b437 tool_dependencies.xml --- a/tool_dependencies.xml Tue Mar 29 08:53:26 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="krona" version="2.6"> - <repository changeset_revision="33c81f965131" name="package_krona_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |