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comparison callaavar.xml @ 8:9def47f3c1e4 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35
author nml
date Tue, 06 Aug 2019 08:50:28 -0400
parents dcd43b402eb3
children 18aad692772a
comparison
equal deleted inserted replaced
7:dcd43b402eb3 8:9def47f3c1e4
1 <tool id="aavariants" name="Amino Acid Variants" version="0.5.1"> 1 <tool id="aavariants" name="Amino Acid Variants" version="0.7.0">
2 <description>Identifies amino acid mutations</description> 2 <description>Identifies amino acid mutations</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.5.1">quasitools</requirement> 4 <requirement type="package" version="0.7.0">quasitools</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 7
8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 8 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&
9 quasitools call aavar $input_bam $ref_file $input_genes 9 quasitools call aavar $input_bam $ref_file $input_genes
46 <param name="var_file" value="nt_variants.vcf" /> 46 <param name="var_file" value="nt_variants.vcf" />
47 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> 47 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
48 <param name="min_freq" value="0.01" /> 48 <param name="min_freq" value="0.01" />
49 <output name="output" > 49 <output name="output" >
50 <assert_contents> 50 <assert_contents>
51 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/> 51 <has_text_matching expression="#CHROM"/>
52 <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." /> 52 <has_text_matching expression="0.0779" />
53 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." /> 53 <has_text_matching expression="0.0103;CAT=.;SRVL=." />
54 <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." /> 54 <has_text_matching expression="0.0163;CAT=.;SRVL=." />
55 <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." /> 55 <has_text_matching expression="0.0148;CAT=.;SRVL=." />
56 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." /> 56 <has_text_matching expression="0.0234;CAT=.;SRVL=." />
57 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." /> 57 <has_text_matching expression="0.0159;CAT=.;SRVL=." />
58 </assert_contents> 58 </assert_contents>
59 </output> 59 </output>
60 </test> 60 </test>
61 </tests> 61 </tests>
62 <help><![CDATA[ 62 <help><![CDATA[