Mercurial > repos > nml > quasitools
comparison callntvar.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="callntvar" name="Nucleotide Variants" version="0.1.0"> | |
| 2 <description>Identifies nucleotide variants</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 call ntvar $input_bam $ref_file | |
| 10 | |
| 11 #if $error_rate: | |
| 12 -e $error_rate | |
| 13 #end if | |
| 14 | |
| 15 -o output.vcf | |
| 16 | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> | |
| 20 <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> | |
| 21 <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.01" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.01."/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="vcf" name="output" from_work_dir="output.vcf" /> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="input_bam" value="align.bam" ftype="bam" /> | |
| 29 <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" /> | |
| 30 <output name="output" > | |
| 31 <assert_contents> | |
| 32 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> | |
| 33 <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s69\sPASS\sDP=157;AC=12;AF=0.0764" /> | |
| 34 </assert_contents> | |
| 35 </output> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help><![CDATA[ | |
| 39 | |
| 40 Nucleotide Variants | |
| 41 =================== | |
| 42 | |
| 43 Call nucleotide variants for a given BAM file and a supplied reference file. | |
| 44 | |
| 45 ]]></help> | |
| 46 <citations> | |
| 47 </citations> | |
| 48 </tool> |