Mercurial > repos > crs4 > taxonomy_krona_chart
comparison taxonomy_krona_chart.xml @ 2:50f204c82159 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart commit 70d4a2d1563e834d8394dce8017a1f0b7ad74f23
author | iuc |
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date | Wed, 02 Mar 2016 04:49:06 -0500 |
parents | 09552faff9c0 |
children | 8e2be617b437 |
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1:09552faff9c0 | 2:50f204c82159 |
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1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.0.0"> | 1 <tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.0"> |
2 <description>from taxonomic profile</description> | 2 <description>from taxonomic profile</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.5">krona</requirement> | 4 <requirement type="package" version="2.6">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> | 7 <command> |
8 <![CDATA[ | 8 <![CDATA[ |
9 | 9 |
10 #if $type_of_data.input[0].is_of_type('taxonomy'): | 10 #if $type_of_data.input[0].is_of_type('taxonomy'): |
11 | 11 |
12 ktImportGalaxy | 12 ktImportGalaxy |
13 -a | |
14 -d "${type_of_data.max_rank}" | 13 -d "${type_of_data.max_rank}" |
15 -n "${root_name}" | 14 -n "${root_name}" |
16 -o ${output} | 15 -o "${output}" |
17 ${combine_inputs} | 16 ${combine_inputs} |
18 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): | 17 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): |
19 "${input_dataset},${input_count}" | 18 "${input_dataset},${input_count}" |
20 #end for | 19 #end for |
21 | 20 |
22 #else: | 21 #else: |
23 | 22 |
24 ktImportText | 23 ktImportText |
25 -a | |
26 -n "${root_name}" | 24 -n "${root_name}" |
27 -o ${output} | 25 -o "${output}" |
28 ${combine_inputs} | 26 ${combine_inputs} |
29 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): | 27 #for $input_count, $input_dataset in enumerate( $type_of_data.input ): |
30 "${input_dataset},${input_count}" | 28 "${input_dataset},${input_count}" |
31 #end for | 29 #end for |
32 | 30 |
33 #end if | 31 #end if |
34 | 32 |
33 && [ -d "${output}.files" ] && ( mkdir "${output.extra_files_path}" && mv "${output}.files" "${output.extra_files_path}/" ) | |
35 ]]> | 34 ]]> |
36 | 35 |
37 </command> | 36 </command> |
38 <inputs> | 37 <inputs> |
39 <conditional name="type_of_data"> | 38 <conditional name="type_of_data"> |
70 </when> | 69 </when> |
71 <when value="text"> | 70 <when value="text"> |
72 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" /> | 71 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" /> |
73 </when> | 72 </when> |
74 </conditional> | 73 </conditional> |
75 <param name="root_name" type="text" size="20" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called "Root""/> | 74 <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called "Root""/> |
76 <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/> | 75 <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/> |
77 </inputs> | 76 </inputs> |
78 <outputs> | 77 <outputs> |
79 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/> | 78 <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/> |
80 </outputs> | 79 </outputs> |
92 **What it does** | 91 **What it does** |
93 | 92 |
94 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. | 93 This tool renders results of a metagenomic profiling as a zoomable pie chart using Krona_. |
95 | 94 |
96 | 95 |
97 .. _Krona: http://sourceforge.net/p/krona/home/krona/ | 96 .. _Krona: https://github.com/marbl/Krona/wiki |
98 | 97 |
99 ------ | 98 ------ |
100 | 99 |
101 **Krona options** | 100 **Krona options** |
102 | 101 |