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1 <tool id="split_paired_reads" name="Split paired end reads" version="1.0.0">
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2 <description></description>
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3 <command interpreter="python">
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4 split_paired_reads.py $input $output1 $output2
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5 </command>
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6 <inputs>
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7 <param name="input" type="data" format="fastqsanger" label="Your paired-end file" />
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8 </inputs>
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9 <outputs>
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10 <data name="output1" format="fastqsanger"/>
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11 <data name="output2" format="fastqsanger"/>
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input" value="3.fastqsanger" ftype="fastqsanger"/>
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16 <output name="output1" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/>
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17 <output name="output2" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/>
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18 </test>
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19 </tests>
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20 <help>
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21
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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 -----
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27
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28 **Input formats**
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29
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30 A multiple-fastq file, for example::
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31
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32 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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33 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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34 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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35 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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36
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37
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38 -----
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39
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40 **Outputs**
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41
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42 One end::
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43
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44 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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45 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
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46 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
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47 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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48
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49 The other end::
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50
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51 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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52 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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53 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
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54 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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55
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56 </help>
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57 </tool>
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