Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 9:148199949636 draft

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Uploaded
author jpetteng
date Fri, 05 Jan 2018 16:25:18 -0500
parents 06e7c1355431
children 5b52b3842765
comparison
equal deleted inserted replaced
8:06e7c1355431 9:148199949636
19 ln -s $jobtype.fastq1 sample_1.fastq; 19 ln -s $jobtype.fastq1 sample_1.fastq;
20 ln -s $jobtype.fastq2 sample_2.fastq; 20 ln -s $jobtype.fastq2 sample_2.fastq;
21 #end if 21 #end if
22 PYTHONPATH=\$PATHONPATH:$__tool_directory__/ecytper/ 22 PYTHONPATH=\$PATHONPATH:$__tool_directory__/ecytper/
23 23
24 $__tool_directory__/bin/ectyper.py 24 $__tool_directory__/ectyper/ectyper.py
25 #if $jobtype.select == "asm" 25 #if $jobtype.select == "asm"
26 -m 4 26 -m 4
27 -i sample.fasta 27 -i sample.fasta
28 #else if $jobtype.select == "se" 28 #else if $jobtype.select == "se"
29 -m 3 29 -m 3