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view callaavar.xml @ 0:71976cfc9022 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
author | nml |
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date | Mon, 04 Dec 2017 10:25:26 -0500 |
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children | a7093d5933a8 |
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<tool id="aavariants" name="Amino Acid Variants" version="0.1.0"> <description>Identifies amino acid mutations</description> <requirements> <requirement type="package" version="0.2.2">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && quasitools call aavar $input_bam $ref_file $var_file $input_genes #if $mutation_db: $mutation_db #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="var_file" type="data" format="vcf" optional="false" label="Variants file" /> <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." /> <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." /> </inputs> <outputs> <data format="vcf" name="output" from_work_dir="output.vcf" /> </outputs> <tests> <test> <param name="input_bam" value="align.bam" /> <param name="ref_file" value="hxb2_pol.fas" /> <param name="var_file" value="nt_variants.vcf" /> <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> <param name="min_freq" value="0.01" /> <output name="output" > <assert_contents> <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/> <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." /> <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." /> <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." /> <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." /> <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." /> <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Amino Acid Variants =================== Identifies amino acid mutations. ]]></help> <citations> </citations> </tool>