Mercurial > repos > nml > quasitools
comparison callcodonvar.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="callcodonvar" name="Codon Variants" version="0.1.0"> | |
| 2 <description>Identifies codon variants and non-synonymous/synonymous mutations</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.2.2">quasitools</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 | |
| 8 cat $input_genes && | |
| 9 | |
| 10 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && | |
| 11 quasitools call codonvar $input_bam $ref_file $offset $input_genes | |
| 12 | |
| 13 #if $error_rate: | |
| 14 -e $error_rate | |
| 15 #end if | |
| 16 | |
| 17 -o output.csv | |
| 18 | |
| 19 ]]></command> | |
| 20 <inputs> | |
| 21 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> | |
| 22 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> | |
| 23 <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/> | |
| 24 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> | |
| 25 <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.01" help="Estimated sequencing error rate. Defaults to 0.01." /> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="csv" name="output" from_work_dir="output.csv" /> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input_bam" value="align.bam" /> | |
| 33 <param name="ref_file" value="hxb2_pol.fas" /> | |
| 34 <param name="offset" value="1269"/> | |
| 35 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> | |
| 36 <output name="output" > | |
| 37 <assert_contents> | |
| 38 <has_text text="#gene,nt position (gene),nt start position,nt end position,ref codon,mutant codon,ref AA,mutant AA,coverage,mutant frequency,mutant type,NS count,S count" /> | |
| 39 <has_text text="RT,1566-2885,1872,1874,aaa,aaC,K,N,154,7.79,NS,1.0000,0.0000" /> | |
| 40 </assert_contents> | |
| 41 </output> | |
| 42 </test> | |
| 43 </tests> | |
| 44 <help><![CDATA[ | |
| 45 | |
| 46 Codon Variants | |
| 47 ============== | |
| 48 | |
| 49 Call codon variants for a given BAM. A report is generated that details nucleotide variants within a | |
| 50 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to | |
| 51 a synonymous or non-synonymous mutation. | |
| 52 | |
| 53 ]]></help> | |
| 54 <citations> | |
| 55 </citations> | |
| 56 </tool> |