Mercurial > repos > nml > quasitools
diff 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 |
parents | |
children | a7093d5933a8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/callaavar.xml Mon Dec 04 10:25:26 2017 -0500 @@ -0,0 +1,59 @@ +<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>