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comparison callaavar.xml @ 0:71976cfc9022 draft

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planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f
author nml
date Mon, 04 Dec 2017 10:25:26 -0500
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-1:000000000000 0:71976cfc9022
1 <tool id="aavariants" name="Amino Acid Variants" version="0.1.0">
2 <description>Identifies amino acid mutations</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 aavar $input_bam $ref_file $var_file $input_genes
10
11 #if $mutation_db:
12 $mutation_db
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="var_file" type="data" format="vcf" optional="false" label="Variants file" />
22 <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
23 <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." />
24 <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." />
25 </inputs>
26 <outputs>
27 <data format="vcf" name="output" from_work_dir="output.vcf" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="input_bam" value="align.bam" />
32 <param name="ref_file" value="hxb2_pol.fas" />
33 <param name="var_file" value="nt_variants.vcf" />
34 <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
35 <param name="min_freq" value="0.01" />
36 <output name="output" >
37 <assert_contents>
38 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/>
39 <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." />
40 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." />
41 <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." />
42 <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." />
43 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." />
44 <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." />
45 </assert_contents>
46 </output>
47 </test>
48 </tests>
49 <help><![CDATA[
50
51 Amino Acid Variants
52 ===================
53
54 Identifies amino acid mutations.
55
56 ]]></help>
57 <citations>
58 </citations>
59 </tool>