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comparison fasta-stats.xml @ 1:16f1f3e2de42 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
author iuc
date Wed, 21 Apr 2021 09:10:46 +0000
parents 9c620a950d3a
children cd0874854f51
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0:9c620a950d3a 1:16f1f3e2de42
1 <tool id="fasta-stats" name="Fasta Statistics" version="1.0.1"> 1 <tool id="fasta-stats" name="Fasta Statistics" version="1.0.2">
2 <description>Display summary statistics for a fasta file.</description> 2 <description>Display summary statistics for a fasta file.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="5.26">perl</requirement> 4 <requirement type="package" version="5.26">perl</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 perl '${__tool_directory__}/fasta-stats.pl' 7 perl '${__tool_directory__}/fasta-stats.pl'
8 '$dataset' 8 '$dataset'
9 #if $genome_size:
10 $genome_size
11 #end if
9 > '$stats' 12 > '$stats'
10 ]]> 13 ]]>
11 </command> 14 </command>
12 <inputs> 15 <inputs>
13 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/> 16 <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
17 <param name="genome_size" type="float" optional="True" label="Genome size estimate (optional)" help="Estimate of the genome size in megabases (MB). If specified, NG50 will be calculated."/>
14 </inputs> 18 </inputs>
15 <outputs> 19 <outputs>
16 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/> 20 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
17 </outputs> 21 </outputs>
18 <tests> 22 <tests>
19 <test> 23 <test>
20 <param name="dataset" value="test.fasta"/> 24 <param name="dataset" value="test.fasta"/>
21 <output name="stats" file="test_out.txt"/> 25 <output name="stats" file="test_out.txt"/>
26 </test>
27 <test>
28 <param name="dataset" value="test.fasta"/>
29 <param name="genome_size" value="5.0"/>
30 <output name="stats" file="ng50_out.txt"/>
22 </test> 31 </test>
23 </tests> 32 </tests>
24 <help> 33 <help>
25 **Fasta Stats** 34 **Fasta Stats**
26 Displays the summary statistics for a fasta file. 35 Displays the summary statistics for a fasta file.
33 Number of base pairs: A, C, G, T, N, Total and Total_not_N 42 Number of base pairs: A, C, G, T, N, Total and Total_not_N
34 43
35 Number of sequences 44 Number of sequences
36 45
37 GC content in % 46 GC content in %
47
48 If an optional genome size estimate is specified, then the NG50 length will also be calculated.
38 49
39 ------ 50 ------
40 51
41 Inputs: 52 Inputs:
42 53