diff test-data/generate_test_data.sh @ 0:2595c27071c2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit 43bbde4f8f8671284b2acb21dfd2657de4ba967f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/generate_test_data.sh	Sat Feb 15 15:32:58 2020 -0500
@@ -0,0 +1,30 @@
+#!/usr/bin/bash
+
+# E. coli locus b0842 (b0842.fasta.gz) downloaded from Enterobase E. coli cgMLST scheme
+# requires: wget, kma, bwa, samtools, bedtools
+
+gunzip b0842.fasta.gz
+
+# Take first 5 alleles to reduce size of test data
+mkdir ecoli_cgMLST
+head -n 10 b0842.fasta > ecoli_cgMLST/ecoli_b0842_1to5.fasta
+
+kma index -k 8 -i ecoli_cgMLST/ecoli_b0842_1to5.fasta -o ecoli_cgMLST/ecoli_b0842_1to5
+
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR884/ERR884056/ERR884056_1.fastq.gz
+
+# Use bwa to map reads to reduced E. coli locus b0842
+# and extract only mapped reads (to reduce size of test dataset)
+bwa index ecoli_cgMLST/ecoli_b0842_1to5.fasta
+
+bwa mem ecoli_cgMLST/ecoli_b0842_1to5.fasta ERR884056_1.fastq.gz -o ERR884056_1_ecoli_b0842_1to5.sam
+
+samtools view ERR884056_1_ecoli_b0842_1to5.sam -bo ERR884056_1_ecoli_b0842_1to5.bam
+
+# Select mapped reads
+samtools view -b -F 4 ERR884056_1_ecoli_b0842_1to5.bam > ERR884056_1_ecoli_b0842_1to5.mapped.bam
+
+samtools sort -n ERR884056_1_ecoli_b0842_1to5.mapped.bam -o ERR884056_1_ecoli_b0842_1to5.mapped.sort.bam
+
+bedtools bamtofastq -i ERR884056_1_ecoli_b0842_1to5.mapped.sort.bam -fq ERR884056_ecoli_b0842.mapped_R1.fastq
+