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0
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1 <tool id="pe_sync" name="pe-sync: Paired-end synchronization check" version="1.0">
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2 <description>The Paired-end synchronization check program determines if the reads in paired-end fastq files are in the proper order (synchronized).</description>
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3 <command interpreter="perl">
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4 pe_sync_2_files.pl $quickcheck $input1 $input2 2>&1 | tee $output
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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 <param name="quickcheck" type="boolean" truevalue="quick" falsevalue="" checked="false" label="Just check a sample of the sequences"
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10 help=""/>
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11 </inputs>
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12 <stdio>
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13 <exit_code range="1:" level="fatal" description="Bad input dataset" />
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14 </stdio>
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15 <outputs>
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16 <data format="txt" name="output" label="pe-sync report for ${input1.name} and ${input2.name}"/>
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17 </outputs>
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18 <tests>
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19 <test>
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1
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20 <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
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21 <param name="input2" ftype="fastq" value="reads2.fastqsanger" />
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22 <param name="quickcheck" value="false"/>
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23 <output name="output">
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24 <assert_contents>
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25 <has_text text="PASSED" />
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26 </assert_contents>
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27 </output>
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0
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28 </test>
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1
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29 <test>
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30 <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
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31 <param name="input2" ftype="fastq" value="reads_unsync_2.fastqsanger" />
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32 <param name="quickcheck" value="false"/>
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33 <output name="output">
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34 <assert_contents>
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35 <has_text text="FAILED" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39
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0
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40 </tests>
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41 <help>
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42 Paired-end read file synchronization checks if left and right reads are in the same order.
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43
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44 The "quick" option will not report the percent of out-of-sync reads
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45 for many failed files, but will run much faster.
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46
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47 This script can handle Casava 1.8.0 style read IDs, and pre 1.8.0 style ids.
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48 Other types of read ID formats may cause a terminal error.
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49
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50 </help>
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51 </tool>
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