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comparison srst2v2.xml @ 3:8bf4865cc3e3 draft

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author estrain
date Sun, 19 May 2019 10:07:05 -0400
parents 6787d952242e
children 65cb7bb11e6b
comparison
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2:6787d952242e 3:8bf4865cc3e3
1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0"> 1 <tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.0">srst2</requirement> 3 <requirement type="package" version="0.2.0">srst2</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6
6 #if $paired_conditional.sPaired == "paired" 7 #if $paired_conditional.sPaired == "paired"
7 ln -s $paired_conditional.fastq1 sample_1.fastq; 8 #if $paired_conditional.fastq1.is_of_type("fastq.gz")
8 ln -s $paired_conditional.fastq2 sample_2.fastq; 9 zcat $paired_conditional.fastq1 > sample_1.fastq;
10 zcat $paired_conditional.fastq2 > sample_2.fastq;
11 #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
12 zcat $paired_conditional.fastq1 > sample_1.fastq;
13 zcat $paired_conditional.fastq2 > sample_2.fastq;
14 #else
15 ln -s $paired_conditional.fastq1 sample_1.fastq;
16 ln -s $paired_conditional.fastq2 sample_2.fastq;
17 #end if
9 #else if $paired_conditional.sPaired == "paired_coll" 18 #else if $paired_conditional.sPaired == "paired_coll"
10 ln -s $paired_conditional.coll.forward sample_1.fastq; 19 #if $paired_conditional.coll.forward.is_of_type("fastq.gz")
11 ln -s $paired_conditional.coll.reverse sample_2.fastq; 20 zcat $paired_conditional.coll.forward > sample_1.fastq;
21 zcat $paired_conditional.coll.reverse > sample_2.fastq;
22 #else if $paired_conditional.coll.forward.is_of_type("fastqsanger.gz")
23 zcat $paired_conditional.coll.forward > sample_1.fastq;
24 zcat $paired_conditional.coll.reverse > sample_2.fastq;
25 #else
26 ln -s $paired_conditional.coll.forward sample_1.fastq;
27 ln -s $paired_conditional.coll.reverse sample_2.fastq;
28 #end if
29 #else if $paired_conditional.sPaired == "single"
30 #if $paired_conditional.fastq1.is_of_type("fastq.gz")
31 zcat $paired_conditional.fastq1 > sample_1.fastq;
32 #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
33 zcat $paired_conditional.fastq1 > sample_1.fastq;
34 #else
35 ln -s $paired_conditional.fastq1 sample_1.fastq;
36 #end if
12 #end if 37 #end if
13 38
14 srst2 39 srst2
15 40
16 #if $paired_conditional.sPaired == "single" 41 #if $paired_conditional.sPaired == "single"
17 --input_se $paired_conditional.fastq1 42 --input_se sample_1.fastq1
18 #else if $paired_conditional.sPaired == "paired" 43 #else
19 --input_pe sample_1.fastq sample_2.fastq
20 #else if $paired_conditional.sPaired == "paired_coll"
21 --input_pe sample_1.fastq sample_2.fastq 44 --input_pe sample_1.fastq sample_2.fastq
22 #end if 45 #end if
23 46
24 --output srst2out 47 --output srst2out
25 --save_scores 48 --save_scores