/tools/fastq/fastq_paired_end_splitter.xml

 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
21Splits 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
23Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
24
25-----
26
27**Input format**
28
29A 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
41Left-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
48Right-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  </help>
56</tool>