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comparison tools/fastq/fastq_paired_end_splitter.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="fastq_paired_end_splitter" name="FASTQ splitter" version="1.0.0">
2 <description>on joined paired end reads</description>
3 <command interpreter="python">fastq_paired_end_splitter.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$output1_file' '$output2_file'</command>
4 <inputs>
5 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" />
6 </inputs>
7 <outputs>
8 <data name="output1_file" format="input" />
9 <data name="output2_file" format="input" />
10 </outputs>
11 <tests>
12 <test>
13 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
14 <output name="output1_file" file="split_pair_reads_1.fastqsanger" />
15 <output name="output2_file" file="split_pair_reads_2.fastqsanger" />
16 </test>
17 </tests>
18 <help>
19 **What it does**
20
21 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.
22
23 Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
24
25 -----
26
27 **Input format**
28
29 A multiple-fastq file, for example::
30
31 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
32 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
33 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
34 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
35
36
37 -----
38
39 **Outputs**
40
41 Left-hand Read::
42
43 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
44 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
45 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
46 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
47
48 Right-hand Read::
49
50 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
51 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
52 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
53 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
54
55 ------
56
57 **Citation**
58
59 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
60
61
62 </help>
63 </tool>