Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 5:a202cc394af8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Hopefully fixed issue with finding ectyper.py
author jpetteng
date Fri, 05 Jan 2018 15:17:46 -0500
parents e07f3859a242
children 06e7c1355431
comparison
equal deleted inserted replaced
4:e07f3859a242 5:a202cc394af8
1 <tool id="ectyper" name="ectyper" version="2.0"> 1 <tool id="ectyper" name="ectyper" version="2.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.6.3">python</requirement> 3 <requirement type="package" version="3.6.3">python</requirement>
4 <requirement type="package">ectyper</requirement>
5 <requirement type="package">biopython</requirement> 4 <requirement type="package">biopython</requirement>
6 <requirement type="package">blast</requirement> 5 <requirement type="package">blast</requirement>
7 <requirement type="package">samtools</requirement> 6 <requirement type="package">samtools</requirement>
8 <requirement type="package">bcftools</requirement> 7 <requirement type="package">bcftools</requirement>
9 <requirement type="package">bowtie</requirement> 8 <requirement type="package">bowtie</requirement>
19 #else if $jobtype.select == "pe" 18 #else if $jobtype.select == "pe"
20 ln -s $jobtype.fastq1 sample_1.fastq; 19 ln -s $jobtype.fastq1 sample_1.fastq;
21 ln -s $jobtype.fastq2 sample_2.fastq; 20 ln -s $jobtype.fastq2 sample_2.fastq;
22 #end if 21 #end if
23 22
24 $__tool_directory__/ectyper.py 23 $__tool_directory__/ectyper/ectyper.py
25 #if $jobtype.select == "asm" 24 #if $jobtype.select == "asm"
26 -m 4 25 -m 4
27 -i sample.fasta 26 -i sample.fasta
28 #else if $jobtype.select == "se" 27 #else if $jobtype.select == "se"
29 -m 3 28 -m 3