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1 <tool id="fastq_join" name="fastq-join" version="1.1.2-484">
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2 <description> - Joins paired-end reads on the overlapping ends</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2-484">ea-utils</requirement>
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5 </requirements>
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6 <command>
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7 fastq-join
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8 -v '$splitChar'
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9 -p $pctMaxDiff
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10 -m $minOverlap
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11 #if $stitchLengthReport:
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12 -r $outputStitchLengthReport
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13 #end if
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14 $read1
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15 $read2
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16 -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined
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17 </command>
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18 <inputs>
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19 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" />
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20 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" />
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21 <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
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22 <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
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23 <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
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24 <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
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25 </inputs>
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26
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27 <outputs>
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28 <data format="input" format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
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29 <data format="input" format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
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30 <data format="input" format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
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31 <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
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32 <filter>stitchLengthReport</filter>
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33 </data>
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34 </outputs>
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35
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36 <stdio>
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37 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
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38 </stdio>
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39
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40 <tests>
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41 <test>
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42 <param name="read1" value="test_read1.fastq" />
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43 <param name="read2" value="test_read3.fastq" />
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44 <output name="outputJoined" file="testout.join.fastq" />
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45 <output name="outputUnmatched1" file="testout.un1.fastq" />
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46 <output name="outputUnmatched2" file="testout.un2.fastq" />
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47 </test>
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48 </tests>
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49
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50 <help>
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51 Overview
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52 --------
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53 fastq-join joins two paired-end reads on the overlapping ends.
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54
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55 Split read ids character: Verifies that the 2 files probe id's match up to char C. Use ' ' for Illumina reads.
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56
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57 Maximum difference is the maximum allowed percentage of bases that differ in the matching region.
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58
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59 Minimum overlap is the minimum number of bases that must overlap (with no more than the maximum difference) for reads to be joined.
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60
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61 Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was.
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62
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63 This tool uses sqr(distance)/len for anchored alignment quality algorithm. It's a good measure of anchored alignment quality, akin to squared-deviation for means. This tool uses the fastq-join program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/FastqJoin for details.
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64 </help>
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65 </tool>
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