Mercurial > repos > iuc > fasta_stats
diff fasta-stats.xml @ 0:9c620a950d3a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
author | iuc |
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date | Thu, 22 Nov 2018 04:16:35 -0500 |
parents | |
children | 16f1f3e2de42 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta-stats.xml Thu Nov 22 04:16:35 2018 -0500 @@ -0,0 +1,55 @@ +<tool id="fasta-stats" name="Fasta Statistics" version="1.0.1"> + <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' + > '$stats' + ]]> + </command> + <inputs> + <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/> + </inputs> + <outputs> + <data name="stats" format="tabular" label="${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> + </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 % + +------ + +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 +@UNPUBLISHED{Seemann_Gladman2012, + author = {Torsten Seemann and Simon Gladman}, + title = {Fasta Statistics: Display summary statistics for a fasta file.}, + year =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>