Mercurial > repos > nml > quasitools
view dnds.xml @ 7:dcd43b402eb3 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit ce3f1b19e7e110ff47365c672bc6fa17cce0a314
author | nml |
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date | Fri, 23 Nov 2018 15:43:16 -0500 |
parents | b69e898b8109 |
children | 9def47f3c1e4 |
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<tool id="dnds" name="dNdS Report" version="0.5.1"> <description>Calculate the dN/dS value for each region in a bed file</description> <requirements> <requirement type="package" version="0.5.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ quasitools dnds $csv_file $ref_file $offset -o output.csv ]]></command> <inputs> <param name="csv_file" type="data" format="csv" optional="false" label="CSV file" /> <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/> </inputs> <outputs> <data format="csv" name="output" from_work_dir="output.csv" /> </outputs> <tests> <test> <param name="csv_file" value="mutant_types.csv" /> <param name="ref_file" value="hxb2_pol.fas" /> <output name="output" ftype="csv" > <assert_contents> <has_text_matching expression="#gene,pn,ps,pn_sites,ps_sites,dn/ds"/> <has_text text="RT,0.0334,0.0111,1,1,3.0539" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ dNdS Report =================== Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants). ]]></help> <citations> <citation type="bibtex"> @misc{GitHubquasitoolsdnds, title = {quasitools dnds}, publisher = {phac-nml}, journal = {GitHub repository}, url = {https://github.com/phac-nml/quasitools}, } </citation> </citations> </tool>