Mercurial > repos > estrain > srst2

comparison srst2v2.xml @ 5:53b629d3da68 draft

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Uploaded
author estrain
date Mon, 20 May 2019 13:55:36 -0400
parents 65cb7bb11e6b
children ba3ddf429854
comparison
equal deleted inserted replaced
4:65cb7bb11e6b 5:53b629d3da68
13 zcat $paired_conditional.fastq2 > sample_2.fastq; 13 zcat $paired_conditional.fastq2 > sample_2.fastq;
14 #else 14 #else
15 ln -s $paired_conditional.fastq1 sample_1.fastq; 15 ln -s $paired_conditional.fastq1 sample_1.fastq;
16 ln -s $paired_conditional.fastq2 sample_2.fastq; 16 ln -s $paired_conditional.fastq2 sample_2.fastq;
17 #end if 17 #end if
18 #else if $paired_conditional.sPaired == "paired_coll" 18 #else if $paired_conditional.sPaired == "paired_coll"
19 #if $paired_conditional.coll.forward.is_of_type("fastq.gz") 19 #if $paired_conditional.coll.forward.is_of_type("fastq.gz")
20 zcat $paired_conditional.coll.forward > sample_1.fastq; 20 zcat $paired_conditional.coll.forward > sample_1.fastq;
21 zcat $paired_conditional.coll.reverse > sample_2.fastq; 21 zcat $paired_conditional.coll.reverse > sample_2.fastq;
22 #else if $paired_conditional.coll.forward.is_of_type("fastqsanger.gz") 22 #else if $paired_conditional.coll.forward.is_of_type("fastqsanger.gz")
23 zcat $paired_conditional.coll.forward > sample_1.fastq; 23 zcat $paired_conditional.coll.forward > sample_1.fastq;
24 zcat $paired_conditional.coll.reverse > sample_2.fastq; 24 zcat $paired_conditional.coll.reverse > sample_2.fastq;
25 #else 25 #else
26 ln -s $paired_conditional.coll.forward sample_1.fastq; 26 ln -s $paired_conditional.coll.forward sample_1.fastq;
27 ln -s $paired_conditional.coll.reverse sample_2.fastq; 27 ln -s $paired_conditional.coll.reverse sample_2.fastq;
28 #end if 28 #end if
29 #else if $paired_conditional.sPaired == "single" 29 #else if $paired_conditional.sPaired == "single"
30 #if $paired_conditional.fastq1.is_of_type("fastq.gz") 30 #if $paired_conditional.fastq1.is_of_type("fastq.gz")
31 zcat $paired_conditional.fastq1 > sample_1.fastq; 31 zcat $paired_conditional.fastq1 > sample_1.fastq;
32 #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz") 32 #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
33 zcat $paired_conditional.fastq1 > sample_1.fastq; 33 zcat $paired_conditional.fastq1 > sample_1.fastq;
34 #else 34 #else
37 #end if 37 #end if
38 38
39 srst2 39 srst2
40 40
41 #if $paired_conditional.sPaired == "single" 41 #if $paired_conditional.sPaired == "single"
42 --input_se sample_1.fastq1 42 --input_se sample_1.fastq
43 #else 43 #else
44 --input_pe sample_1.fastq sample_2.fastq 44 --input_pe sample_1.fastq sample_2.fastq
45 #end if 45 #end if
46 46
47 --output srst2out 47 --output srst2out