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comparison fastq-join.xml @ 1:593a729e5706 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit 394834f8f34909961cfbf6252fefbdc63342d78d
author lparsons
date Mon, 13 Jul 2015 11:45:19 -0400
parents 2ac846969812
children b007d9642911
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0:2ac846969812 1:593a729e5706
1 <tool id="fastq_join" name="fastq-join" version="1.1.2-484"> 1 <tool id="fastq_join" name="fastq-join" version="0.1.1">
2 <description> - Joins paired-end reads on the overlapping ends</description> 2 <description> - Joins two paired-end reads on the overlapping ends</description>
3
3 <requirements> 4 <requirements>
4 <requirement type="package" version="1.1.2-484">ea-utils</requirement> 5 <requirement type="package" version="1.1.2-484">ea-utils</requirement>
5 </requirements> 6 </requirements>
6 <command> 7
7 fastq-join 8 <stdio>
9 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
10 </stdio>
11
12 <command><![CDATA[
13 fastq-join
8 -v '$splitChar' 14 -v '$splitChar'
9 -p $pctMaxDiff 15 -p $pctMaxDiff
10 -m $minOverlap 16 -m $minOverlap
11 #if $stitchLengthReport: 17 #if $stitchLengthReport:
12 -r $outputStitchLengthReport 18 -r $outputStitchLengthReport
13 #end if 19 #end if
14 $read1 20 $read1
15 $read2 21 $read2
16 -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined 22 -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined
23 ]]>
17 </command> 24 </command>
25
18 <inputs> 26 <inputs>
19 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" /> 27 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" />
20 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" /> 28 <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" />
21 <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" /> 29 <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" />
22 <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" /> 30 <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" />
23 <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" /> 31 <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" />
24 <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" /> 32 <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" />
25 </inputs> 33 </inputs>
26 34
27 <outputs> 35 <outputs>
28 <data format="input" format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/> 36 <data format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
29 <data format="input" format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/> 37 <data format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
30 <data format="input" format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/> 38 <data format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
31 <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)"> 39 <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
32 <filter>stitchLengthReport</filter> 40 <filter>stitchLengthReport</filter>
33 </data> 41 </data>
34 </outputs> 42 </outputs>
35
36 <stdio>
37 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
38 </stdio>
39 43
40 <tests> 44 <tests>
41 <test> 45 <test>
42 <param name="read1" value="test_read1.fastq" /> 46 <param name="read1" value="test_read1.fastq" />
43 <param name="read2" value="test_read3.fastq" /> 47 <param name="read2" value="test_read3.fastq" />
45 <output name="outputUnmatched1" file="testout.un1.fastq" /> 49 <output name="outputUnmatched1" file="testout.un1.fastq" />
46 <output name="outputUnmatched2" file="testout.un2.fastq" /> 50 <output name="outputUnmatched2" file="testout.un2.fastq" />
47 </test> 51 </test>
48 </tests> 52 </tests>
49 53
50 <help> 54 <help><![CDATA[
51 Overview 55 Overview
52 -------- 56 --------
53 fastq-join joins two paired-end reads on the overlapping ends. 57 fastq-join joins two paired-end reads on the overlapping ends.
54 58
55 Split read ids character: Verifies that the 2 files probe id's match up to char C. Use ' ' for Illumina reads. 59 Split read ids character: Verifies that the 2 files probe id's match up to char C. Use ' ' for Illumina reads.
59 Minimum overlap is the minimum number of bases that must overlap (with no more than the maximum difference) for reads to be joined. 63 Minimum overlap is the minimum number of bases that must overlap (with no more than the maximum difference) for reads to be joined.
60 64
61 Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was. 65 Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was.
62 66
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. 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.
68 ]]>
64 </help> 69 </help>
70
71 <citations>
72 <citation type="bibtex">
73 @article{aronesty_comparison_2013,
74 title = {Comparison of {Sequencing} {Utility} {Programs}},
75 volume = {7},
76 issn = {18750362},
77 url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1},
78 doi = {10.2174/1875036201307010001},
79 language = {en},
80 number = {1},
81 urldate = {2015-07-10},
82 journal = {The Open Bioinformatics Journal},
83 author = {Aronesty, Erik},
84 month = jan,
85 year = {2013},
86 pages = {1--8}
87 }
88 </citation>
89 </citations>
90
65 </tool> 91 </tool>