Mercurial > repos > iuc > fasta_stats
view fasta-stats.xml @ 3:56022eb50bbd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit ecd37d0702cbe5cf9fa244c129a008b039d5e164"
author | iuc |
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date | Mon, 05 Jul 2021 13:36:26 +0000 |
parents | cd0874854f51 |
children | 0dbb995c7d35 |
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<tool id="fasta-stats" name="Fasta Statistics" version="1.0.3"> <description>Display summary statistics for a fasta file.</description> <requirements> <requirement type="package" version="5.26">perl</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ perl '${__tool_directory__}/fasta-stats.pl' '$dataset' #if $genome_size: $genome_size #end if > '$stats' ]]> </command> <inputs> <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/> <param name="genome_size" type="float" optional="True" label="Genome size estimate (optional)" help="Estimate of the genome size in bases. If specified, NG50 and LG50 will be calculated."/> </inputs> <outputs> <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/> </outputs> <tests> <test> <param name="dataset" value="test.fasta"/> <output name="stats" file="test_out.txt"/> </test> <test> <param name="dataset" value="ng50_input.fasta"/> <param name="genome_size" value="4000"/> <output name="stats" file="ng50_out.txt"/> </test> </tests> <help> **Fasta Stats** Displays the summary statistics for a fasta file. ------ Outputs in tabular form: Lengths: n50, min, max, median and average Number of base pairs: A, C, G, T, N, Total and Total_not_N Number of sequences GC content in % If an optional genome size estimate is specified, then the NG50 length will also be calculated. ------ Inputs: Fasta dataset </help> <citations> <citation type="bibtex"> @UNPUBLISHED{Seemann_Gladman2012, author = {Torsten Seemann and Simon Gladman}, title = {Fasta Statistics: Display summary statistics for a fasta file.}, year = {2012}, url = {https://github.com/galaxyproject/tools-iuc}, } </citation> </citations> </tool>