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