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1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="1.0.0">
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2 <description>on paired end reads</description>
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3 <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file'</command>
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4 <inputs>
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5 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" />
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6 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" />
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7 </inputs>
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8 <outputs>
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9 <data name="output_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="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
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14 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
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15 <output name="output_file" file="3.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 This tool joins paired end FASTQ reads from two separate files into a single read in one file. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is excluded from the output.
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22
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23 Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user.
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24
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25 -----
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26
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27 **Input formats**
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28
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29 Left-hand Read::
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30
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31 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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32 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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33 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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34 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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35
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36 Right-hand Read::
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37
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38 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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39 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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40 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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41 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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42
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43 -----
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44
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45 **Output**
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46
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47 A multiple-fastq file, for example::
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48
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49 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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50 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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51 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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52 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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53
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54 ------
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55
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56 **Citation**
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57
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58 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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59
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60
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61 </help>
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62 </tool>
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