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annotate fastq-join.xml @ 2:b007d9642911 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:36:11 -0400
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1 <tool id="fastq_join" name="fastq-join" version="1.1.2-806">
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2 <description> - Joins two paired-end reads on the overlapping ends</description>
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4 <requirements>
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5 <requirement type="package" version="1.1.2-806">ea-utils</requirement>
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6 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
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10 </stdio>
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12 <command><![CDATA[
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13 fastq-join
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14 -v '$splitChar'
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15 -p $pctMaxDiff
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16 -m $minOverlap
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17 #if $stitchLengthReport:
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18 -r $outputStitchLengthReport
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19 #end if
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20 $read1
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21 $read2
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22 -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined
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23 ]]>
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24 </command>
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25
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26 <inputs>
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27 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" />
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28 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" />
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29 <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
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30 <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
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31 <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
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32 <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
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33 </inputs>
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34
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35 <outputs>
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36 <data format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
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37 <data format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
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38 <data format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
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39 <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
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40 <filter>stitchLengthReport</filter>
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41 </data>
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42 </outputs>
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43
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44 <tests>
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45 <test>
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46 <param name="read1" value="test_read1.fastq" />
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47 <param name="read2" value="test_read3.fastq" />
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48 <output name="outputJoined" file="testout.join.fastq" />
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49 <output name="outputUnmatched1" file="testout.un1.fastq" />
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50 <output name="outputUnmatched2" file="testout.un2.fastq" />
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51 </test>
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52 </tests>
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53
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54 <help><![CDATA[
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55 Overview
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56 --------
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57 fastq-join joins two paired-end reads on the overlapping ends.
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58
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59 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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60
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61 Maximum difference is the maximum allowed percentage of bases that differ in the matching region.
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62
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63 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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64
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65 Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was.
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66
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67 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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68 ]]>
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69 </help>
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71 <citations>
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72 <citation type="bibtex">
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73 @article{aronesty_comparison_2013,
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74 title = {Comparison of {Sequencing} {Utility} {Programs}},
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75 volume = {7},
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76 issn = {18750362},
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77 url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1},
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78 doi = {10.2174/1875036201307010001},
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79 language = {en},
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80 number = {1},
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81 urldate = {2015-07-10},
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82 journal = {The Open Bioinformatics Journal},
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83 author = {Aronesty, Erik},
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84 month = jan,
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85 year = {2013},
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86 pages = {1--8}
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87 }
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88 </citation>
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89 </citations>
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90
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91 </tool>