Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 22:54ae509ceeef draft

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author jpetteng
date Sun, 07 Jan 2018 15:05:41 -0500
parents 876b99d07203
children 41301e1f075a
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21:876b99d07203 22:54ae509ceeef
19 #else if $jobtype.select == "pe" 19 #else if $jobtype.select == "pe"
20 ln -s $jobtype.fastq1 sample_1.fastq; 20 ln -s $jobtype.fastq1 sample_1.fastq;
21 ln -s $jobtype.fastq2 sample_2.fastq; 21 ln -s $jobtype.fastq2 sample_2.fastq;
22 #end if 22 #end if
23 23
24 $__tool_directory__/bin/ectyper 24 python $__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