Mercurial > repos > iuc > fasta_stats
comparison fasta-stats.xml @ 1:16f1f3e2de42 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit 02d0ae7ac02425ef454d2e42a0513887596a3b4d"
author | iuc |
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date | Wed, 21 Apr 2021 09:10:46 +0000 |
parents | 9c620a950d3a |
children | cd0874854f51 |
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0:9c620a950d3a | 1:16f1f3e2de42 |
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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 |