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comparison split_paired_reads.xml @ 0:36163bff76cc draft default tip

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author devteam
date Wed, 25 Sep 2013 11:29:58 -0400
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1 <tool id="split_paired_reads" name="Split paired end reads" version="1.0.0">
2 <description></description>
3 <command interpreter="python">
4 split_paired_reads.py $input $output1 $output2
5 </command>
6 <inputs>
7 <param name="input" type="data" format="fastqsanger" label="Your paired-end file" />
8 </inputs>
9 <outputs>
10 <data name="output1" format="fastqsanger"/>
11 <data name="output2" format="fastqsanger"/>
12 </outputs>
13 <tests>
14 <test>
15 <param name="input" value="3.fastqsanger" ftype="fastqsanger"/>
16 <output name="output1" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/>
17 <output name="output2" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/>
18 </test>
19 </tests>
20 <help>
21
22 **What it does**
23
24 Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length.
25
26 -----
27
28 **Input formats**
29
30 A multiple-fastq file, for example::
31
32 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
33 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
34 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
35 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
36
37
38 -----
39
40 **Outputs**
41
42 One end::
43
44 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
45 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
46 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
47 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
48
49 The other end::
50
51 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
52 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
53 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
54 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
55
56 </help>
57 </tool>