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
date Wed, 02 Mar 2016 04:49:06 -0500
parents 09552faff9c0
children 8e2be617b437
comparison
equal deleted inserted replaced
1:09552faff9c0 2:50f204c82159
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" "${output.extra_files_path}/" )
35 ]]> 34 ]]>
36 35
37 </command> 36 </command>
38 <inputs> 37 <inputs>
39 <conditional name="type_of_data"> 38 <conditional name="type_of_data">
70 </when> 69 </when>
71 <when value="text"> 70 <when value="text">
72 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" /> 71 <param name="input" type="data" format="tabular" multiple="True" label="Input file" help="Select a MetaPhlAn dataset" />
73 </when> 72 </when>
74 </conditional> 73 </conditional>
75 <param name="root_name" type="text" size="20" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/> 74 <param name="root_name" type="text" value="Root" label="Provide a name for the basal rank" help="-n; Otherwise it will simply be called &quot;Root&quot;"/>
76 <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/> 75 <param name="combine_inputs" type="boolean" truevalue="-c" falsevalue="" selected="False" label="Combine data from multiple datasets?" help="-c; Combine data from each dataset, rather than creating separate datasets within the chart"/>
77 </inputs> 76 </inputs>
78 <outputs> 77 <outputs>
79 <data format="html" name="output" label="${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