Mercurial > repos > nml > quasitools
comparison drmutations.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="drmutations" name="Drug Resistance Mutations" version="0.1.0"> | |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.2.2">quasitools</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 | |
| 8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && | |
| 9 quasitools drmutations $input_bam $ref_file $var_file $input_genes | |
| 10 | |
| 11 #if $mutation_db: | |
| 12 $mutation_db | |
| 13 #end if | |
| 14 | |
| 15 #if $min_freq: | |
| 16 -f $min_freq | |
| 17 #end if | |
| 18 | |
| 19 #if $reporting_thres: | |
| 20 -t $reporting_thres | |
| 21 #end if | |
| 22 | |
| 23 -o output.csv | |
| 24 | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> | |
| 28 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> | |
| 29 <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" /> | |
| 30 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> | |
| 31 <param name="mutation_db" type="data" format="tsv" optional="false" label="Mutation DB" /> | |
| 32 <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." /> | |
| 33 <param name="reporting_thres" type="integer" min="1" max="20" optional="true" label="Reporting threshold" value="1" | |
| 34 help="The minimum percentage required for an entry in the drug resistant report. Defaults to 1."/> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data format="csv" name="output" from_work_dir="output.csv" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 <param name="input_bam" value="align.bam" /> | |
| 42 <param name="ref_file" value="hxb2_pol.fas" /> | |
| 43 <param name="var_file" value="nt_variants.vcf" /> | |
| 44 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> | |
| 45 <param name="mutation_db" value="mutation_db.tsv" /> | |
| 46 <output name="output" > | |
| 47 <assert_contents> | |
| 48 <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" /> | |
| 49 <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,7.79,154" /> | |
| 50 </assert_contents> | |
| 51 </output> | |
| 52 </test> | |
| 53 </tests> | |
| 54 <help><![CDATA[ | |
| 55 | |
| 56 Drug Resistance Mutations | |
| 57 ========================= | |
| 58 | |
| 59 Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%). | |
| 60 | |
| 61 ]]></help> | |
| 62 <citations> | |
| 63 </citations> | |
| 64 </tool> |