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view callntvar.xml @ 8:9def47f3c1e4 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
author | nml |
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date | Tue, 06 Aug 2019 08:50:28 -0400 |
parents | dcd43b402eb3 |
children | 18aad692772a |
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<tool id="callntvar" name="Nucleotide Variants" version="0.7.0"> <description>Identifies nucleotide variants</description> <requirements> <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && quasitools call ntvar $input_bam $ref_file #if $error_rate: -e $error_rate #end if -o output.vcf ]]></command> <inputs> <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.0021" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.0021."/> </inputs> <outputs> <data format="vcf" name="output" from_work_dir="output.vcf" /> </outputs> <tests> <test> <param name="input_bam" value="align.bam" ftype="bam" /> <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" /> <output name="output" > <assert_contents> <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s100\sPASS\sDP=157;AC=12;AF=0.0764" /> <has_text_matching expression="hxb2_pol\s812\s.\sg\sa\s58\sPASS\sDP=634;AC=10;AF=0.0158" /> <has_text_matching expression="hxb2_pol\s2278\s.\sc\st\s54\sPASS\sDP=557;AC=9;AF=0.0162" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Nucleotide Variants =================== Call nucleotide variants for a given BAM file and a supplied reference file. ]]></help> <citations> <citation type="bibtex"> @misc{GitHubquasitoolscallntvar, title = {quasitools callntvar}, publisher = {phac-nml}, journal = {GitHub repository}, url = {https://github.com/phac-nml/quasitools}, } </citation> </citations> </tool>