Mercurial > repos > lparsons > fastq_join

annotate fastq-join.xml @ 3:8ec3dfde378b draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit a7f8461032de196092033c9ceae9f4407a469c44
author lparsons
date Wed, 16 Dec 2015 16:01:08 -0500
parents b007d9642911
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1 <tool id="fastq_join" name="fastq-join" version="1.1.2-806.1">
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2 <description> - Joins two paired-end reads on the overlapping ends</description>
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3
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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 #if str( $input_type.input_type_selector ) == 'paired':
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21 "${input_type.read1}"
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22 "${input_type.read2}"
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23 #else:
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24 "${input_type.input_collection.forward}"
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25 "${input_type.input_collection.reverse}"
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26 #end if
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27 -o "${outputUnmatched1}" -o "${outputUnmatched2}" -o "${outputJoined}"
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28 ]]>
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29 </command>
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30
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31 <inputs>
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32 <conditional name="input_type">
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33 <param name="input_type_selector" type="select" label="Dataset type">
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34 <option value="paired">Paired-end</option>
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35 <option value="paired_collection">Paired-end Dataset Collection</option>
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36 </param>
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37 <when value="paired">
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38 <param format="fastqsanger" name="read1" type="data" label="Read 1 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
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39 <param format="fastqsanger" name="read2" type="data" label="Read 2 Fastq" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
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40 </when>
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41 <when value="paired_collection">
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42 <param name="input_collection" format="fastqsanger"
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43 type="data_collection" collection_type="paired"
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44 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values with offset 33 (fastqsanger)." />
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45 </when>
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46 </conditional>
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47 <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
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48 <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
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49 <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
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50 <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
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51 </inputs>
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52
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53 <outputs>
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54 <data format="fastqsanger" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
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55 <data format="fastqsanger" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
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56 <data format="fastqsanger" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
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57 <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
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58 <filter>stitchLengthReport</filter>
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59 </data>
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60 </outputs>
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61
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62 <tests>
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63 <test>
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64 <param name="read1" value="test_read1.fastq" ftype="fastqsanger" />
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65 <param name="read2" value="test_read3.fastq" ftype="fastqsanger" />
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66 <output name="outputJoined" file="testout.join.fastq" />
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67 <output name="outputUnmatched1" file="testout.un1.fastq" />
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68 <output name="outputUnmatched2" file="testout.un2.fastq" />
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69 </test>
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70 </tests>
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71
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72 <help><![CDATA[
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73 Overview
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74 --------
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75 fastq-join joins two paired-end reads on the overlapping ends.
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76
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77 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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78
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79 Maximum difference is the maximum allowed percentage of bases that differ in the matching region.
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80
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81 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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82
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83 Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was.
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84
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85 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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86 ]]>
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87 </help>
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88
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89 <citations>
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90 <citation type="bibtex">
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91 @article{aronesty_comparison_2013,
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92 title = {Comparison of {Sequencing} {Utility} {Programs}},
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93 volume = {7},
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94 issn = {18750362},
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95 url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1},
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96 doi = {10.2174/1875036201307010001},
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97 language = {en},
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98 number = {1},
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99 urldate = {2015-07-10},
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100 journal = {The Open Bioinformatics Journal},
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101 author = {Aronesty, Erik},
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102 month = jan,
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103 year = {2013},
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104 pages = {1--8}
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105 }
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106 </citation>
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107 </citations>
593a729e5706 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit 394834f8f34909961cfbf6252fefbdc63342d78d
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108
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2ac846969812 Uploaded initial version with package dependency
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109 </tool>