Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 8:06e7c1355431 draft

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Uploaded
author jpetteng
date Fri, 05 Jan 2018 16:21:19 -0500
parents a202cc394af8
children 148199949636
comparison
equal deleted inserted replaced
7:b9146bf9de08 8:06e7c1355431
17 ln -s $jobtype.fastq1 sample_1.fastq; 17 ln -s $jobtype.fastq1 sample_1.fastq;
18 #else if $jobtype.select == "pe" 18 #else if $jobtype.select == "pe"
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 23
23 $__tool_directory__/ectyper/ectyper.py 24 $__tool_directory__/bin/ectyper.py
24 #if $jobtype.select == "asm" 25 #if $jobtype.select == "asm"
25 -m 4 26 -m 4
26 -i sample.fasta 27 -i sample.fasta
27 #else if $jobtype.select == "se" 28 #else if $jobtype.select == "se"
28 -m 3 29 -m 3