Mercurial > repos > nml > quasitools
comparison dnds.xml @ 0:71976cfc9022 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
| author | nml |
|---|---|
| date | Mon, 04 Dec 2017 10:25:26 -0500 |
| parents | |
| children | a7093d5933a8 |
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| -1:000000000000 | 0:71976cfc9022 |
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| 1 <tool id="dnds" name="dNdS Report" version="0.1.0"> | |
| 2 <description>Calculate the dN/dS value for each region in a bed file</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.2.2">quasitools</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 | |
| 8 quasitools dnds $csv_file $ref_file $offset -o output.csv | |
| 9 | |
| 10 ]]></command> | |
| 11 <inputs> | |
| 12 <param name="csv_file" type="data" format="csv" optional="false" label="CSV file" /> | |
| 13 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> | |
| 14 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="csv" name="output" from_work_dir="output.csv" /> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="csv_file" value="mutant_types.csv" /> | |
| 22 <param name="ref_file" value="hxb2_pol.fas" /> | |
| 23 <output name="output" ftype="csv" > | |
| 24 <assert_contents> | |
| 25 <has_text_matching expression="#gene,pn,ps,pn_sites,ps_sites,dn/ds"/> | |
| 26 <has_text text="RT,0.0334,0.0111,1,1,3.0539" /> | |
| 27 </assert_contents> | |
| 28 </output> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help><![CDATA[ | |
| 32 | |
| 33 dNdS Report | |
| 34 =================== | |
| 35 | |
| 36 Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants). | |
| 37 | |
| 38 ]]></help> | |
| 39 <citations> | |
| 40 </citations> | |
| 41 </tool> |