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comparison microrunqc.xml @ 13:59e137488c63 draft

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author estrain
date Wed, 24 May 2023 17:24:23 +0000
parents 50867379763d
children c3eb197a283b
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12:50867379763d 13:59e137488c63
1 <tool id="microrunqc" name="microrunqc" version="1.0.0"> 1 <tool id="microrunqc" name="microrunqc" version="1.0.1">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.4.0">skesa</requirement> 4 <requirement type="package" version="2.4.0">skesa</requirement>
5 <requirement type="package" version="2.23.0">mlst</requirement> 5 <requirement type="package" version="2.23.0">mlst</requirement>
6 <requirement type="package" version="0.7.17">bwa</requirement> 6 <requirement type="package" version="0.7.17">bwa</requirement>
101 #end if 101 #end if
102 #if $options.minscore 102 #if $options.minscore
103 --minscore $options.minscore 103 --minscore $options.minscore
104 #end if 104 #end if
105 #end if 105 #end if
106 ${outname}.fasta > ${outname}.mlst.tsv; 106 ${outname}.fasta > ${outname}.mlst_raw.tsv;
107
108 perl mlstAddFields.pl ${outname}.mlst_raw.tsv > ${outname}.mlst.tsv;
107 109
108 python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan}; 110 python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan};
109 111
110 python $__tool_directory__/sum_mlst.py --fasta ${outname}.fasta --mlst ${outname}.mlst.tsv --med insert.median --fqscan fq_out.tab --out sum_qc.txt 112 python $__tool_directory__/sum_mlst.py --fasta ${outname}.fasta --mlst ${outname}.mlst.tsv --med insert.median --fqscan fq_out.tab --out sum_qc.txt
111 113