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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 <requirements>
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4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <command interpreter="python">fastq_paired_end_splitter.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$output1_file' '$output2_file'</command>
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7 <inputs>
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8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" />
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9 </inputs>
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10 <outputs>
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11 <data name="output1_file" format="input" />
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12 <data name="output2_file" format="input" />
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13 </outputs>
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14 <tests>
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15 <test>
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16 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
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17 <output name="output1_file" file="split_pair_reads_1.fastqsanger" />
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18 <output name="output2_file" file="split_pair_reads_2.fastqsanger" />
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19 </test>
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20 </tests>
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21 <help>
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22 **What it does**
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23
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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.
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25
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26 Sequence identifiers will have /1 or /2 appended for the split left-hand and right-hand reads, respectively.
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27
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28 -----
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29
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30 **Input format**
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31
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32 A multiple-fastq file, for example::
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33
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34 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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35 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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36 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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37 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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38
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39
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40 -----
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41
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42 **Outputs**
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43
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44 Left-hand Read::
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45
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46 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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47 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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48 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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49 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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50
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51 Right-hand Read::
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52
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53 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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54 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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55 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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56 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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57
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58 ------
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59
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60 **Citation**
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61
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62 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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63
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64
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65 </help>
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66 </tool>
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