Mercurial > repos > estrain > microrunqc
comparison microrunqc.xml @ 13:59e137488c63 draft
Uploaded
author | estrain |
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date | Wed, 24 May 2023 17:24:23 +0000 |
parents | 50867379763d |
children | c3eb197a283b |
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12:50867379763d | 13:59e137488c63 |
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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 |