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planemo upload for repository https://github.com/galaxyproject/tools-iuc/kmer2stats/ commit 069a351be3e6272c2d511c545593f32fd18f8a84
author iuc
date Tue, 22 Apr 2025 11:34:43 +0000
parents 6150c3b0a1eb
children
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0:6150c3b0a1eb 1:ee32f1a3b2a7
1 <tool id="kmer2stats" name="Kmer2Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> 1 <tool id="kmer2stats" name="Kmer2Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
2 <description>A tool for creating data files for statistics based on kmers</description> 2 <description>A tool that computes kmer alpha diversity metrics and other statistics</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.1</token> 4 <token name="@TOOL_VERSION@">1.0.1</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">kmer2stats</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">kmer2stats</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
17 </command> 17 </command>
18 <inputs> 18 <inputs>
19 <param name="input_file" type="data" format="tabular,txt" label="File input"/> 19 <param name="input_file" type="data" format="tabular,txt" label="File input"/>
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="output_file" format="csv" label="${tool.name}: COMPUTED DIVERSITY"/> 22 <data name="output_file" format="tabular" label="${tool.name}: kmer statistics"/>
23 </outputs> 23 </outputs>
24 <tests> 24 <tests>
25 <test expect_num_outputs="1"> 25 <test expect_num_outputs="1">
26 <param name="input_file" ftype="txt" value="test_file.txt"/> 26 <param name="input_file" ftype="txt" value="test_file.txt"/>
27 <output name="output_file" ftype="csv" value="compute_diversity.csv"/> 27 <output name="output_file" ftype="tabular" value="compute_diversity.csv"/>
28 </test> 28 </test>
29 </tests> 29 </tests>
30 <help> 30 <help>
31 <![CDATA[ 31 <![CDATA[
32 32
33 **What this do** 33 **What this tool does**
34 34
35 This tool calculates diversity based on counted kmers. 35 This tool calculates alpha diversity metrics and other statistics such as observed features based on counted kmers.
36 36
37 **Input** 37 **Input**
38 38
39 This tool was designed to use the output from jellyfish but it also can take a file which should look like this: 39 This tool was designed to use the output from jellyfish but it also can take any file that looks like this:
40 40
41 :: 41 ::
42 42
43 ANYTHING SINCE THIS LINE WILL ALWAYS BE SKIPPED 43 ANYTHING SINCE THIS LINE WILL ALWAYS BE SKIPPED
44 AAAAAA 8453 44 AAAAAA 8453
63 63
64 The first line will always be skipped so be sure to start the counted kmers in the second row! 64 The first line will always be skipped so be sure to start the counted kmers in the second row!
65 65
66 **Output** 66 **Output**
67 67
68 This will be a file where the alpha diversity is calculated and stored as a panda dataframe which then can be used for plotting. 68 Two column table with metric name in the first column and value in second column.
69 69
70 ::
71
72 Metric Value
73 shannon 3.0008343481203097
74 simpson_d 0.05166872360281036
75 pielou_e 0.9856502651904311
76
70 ]]> 77 ]]>
71 </help> 78 </help>
72 <citations> 79 <citations>
73 <citation type="bibtex">@misc{BibEntry2025Apr, 80 <citation type="bibtex">@misc{BibEntry2025Apr,
74 title = {{kmer2stats}}, 81 title = {{kmer2stats}},