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1 <tool id="resync" name="resync: Paired-end resynchronization" version="1.0">
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2 <description>Resynchronize a pair of paired-end fastq files</description>
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3 <command interpreter="perl">
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4 resync.pl $input1 $input2 $output1 $output2
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5 </command>
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6 <inputs>
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7 <param name="input1" type="data" format="fastq" label="Input 1"/>
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8 <param name="input2" type="data" format="fastq" label="Input 2"/>
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9 </inputs>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" description="Bad input dataset" />
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12 </stdio>
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13 <outputs>
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14 <data format_source="input1" name="output1" label="resync ${input1.name}"/>
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15 <data format_source="input2" name="output2" label="resync ${input2.name}"/>
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16 </outputs>
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17 <tests>
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18 <test>
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1
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19 <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
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20 <param name="input2" ftype="fastq" value="reads2.fastqsanger" />
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21 <!-- synchronized files should remain unchanged -->
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22 <output name="output1" file="reads1.fastqsanger" />
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23 <output name="output2" file="reads2.fastqsanger" />
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24 </test>
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25 <test>
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26 <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
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27 <param name="input2" ftype="fastq" value="reads_unsync_2.fastqsanger" />
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28 <output name="output1">
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29 <!-- unsynchronized files should remove unpaired read -->
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30 <assert_contents>
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31 <has_text text="@HWUSI-EAS1737:7:1:4411:1170#CAGATC/1" />
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32 <not_has_text text="@HWUSI-EAS1737:7:1:16187:1196#CAGATC/1" />
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33 </assert_contents>
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34 </output>
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35 <output name="output2">
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36 <!-- unsynchronized files should remove unpaired read -->
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37 <assert_contents>
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38 <has_text text="@HWUSI-EAS1737:7:1:4411:1170#CAGATC/2" />
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39 <not_has_text text="@HWUSI-EAS1737:7:1:16187:1196#CAGATC/2" />
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40 </assert_contents>
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41 </output>
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0
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42 </test>
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43 </tests>
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44 <help>
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45 Resynchronize a pair of paired-end fastq files.
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46
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47 Reads in two potentially unsynchronized fastq files and writes out two synchronized fastq files.
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48
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49 This script can handle Casava 1.8.0 style read IDs, and pre 1.8.0 style ids.
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50 Other types of read ID formats may cause a terminal error.
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51
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52 The synchronized files have properly paired reads, with singelton reads removed.
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53
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54 </help>
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55 </tool>
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