Mercurial > repos > devteam > fastq_paired_end_joiner
annotate fastq_paired_end_joiner.xml @ 2:41ab1243e8f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:42:03 -0500 |
| parents | 270a8ed8a300 |
| children | 6a7f5da7c76d |
| rev | line source |
|---|---|
| 1 | 1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.0"> |
| 0 | 2 <description>on paired end reads</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | |
| 5 </requirements> | |
| 1 | 6 <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style'</command> |
| 0 | 7 <inputs> |
| 8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" /> | |
| 9 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" /> | |
| 1 | 10 <param name="style" type="select" label="FASTQ Header Style"> |
| 11 <option value="old" selected="true">old</option> | |
| 12 <option value="new">new</option> | |
| 13 </param> | |
| 0 | 14 </inputs> |
| 15 <outputs> | |
| 16 <data name="output_file" format="input" /> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" /> | |
| 21 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" /> | |
| 22 <output name="output_file" file="3.fastqsanger" /> | |
| 23 </test> | |
| 24 </tests> | |
| 25 <help> | |
| 26 **What it does** | |
| 27 | |
| 1 | 28 This tool joins paired end FASTQ reads from two separate files into a |
| 29 single read in one file. The join is performed using sequence | |
| 30 identifiers, allowing the two files to contain differing ordering. If | |
| 31 a sequence identifier does not appear in both files, it is excluded | |
| 32 from the output. | |
| 0 | 33 |
| 34 ----- | |
| 35 | |
| 36 **Input formats** | |
| 37 | |
| 1 | 38 Both old and new (from recent Illumina software) style FASTQ headers |
| 39 are supported. The following example uses the "old" style. | |
| 40 | |
| 0 | 41 Left-hand Read:: |
| 42 | |
| 43 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 | |
| 44 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC | |
| 45 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 | |
| 46 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh | |
| 47 | |
| 48 Right-hand Read:: | |
| 49 | |
| 50 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | |
| 51 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | |
| 52 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | |
| 53 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | |
| 54 | |
| 55 ----- | |
| 56 | |
| 57 **Output** | |
| 58 | |
| 59 A multiple-fastq file, for example:: | |
| 60 | |
| 61 @HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
| 62 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | |
| 63 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
| 64 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | |
| 65 | |
| 66 ------ | |
| 67 | |
| 1 | 68 **The "new" style** |
| 69 | |
| 70 Recent Illumina FASTQ headers are structured as follows:: | |
| 71 | |
| 72 @COORDS FLAGS | |
| 73 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y | |
| 74 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE | |
| 75 | |
| 76 where the whitespace character between COORDS and FLAGS can be either | |
| 77 a space or a tab. | |
| 0 | 78 |
| 1 | 79 ------ |
| 80 | |
| 81 **Credits** | |
| 0 | 82 |
| 1 | 83 This is an extended version (adds support for "new" style FASTQ headers) |
| 84 of D. Blankenberg's fastq joiner: | |
| 0 | 85 |
| 1 | 86 `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ |
| 87 | |
| 88 New style header support added by Simone Leo <simone.leo@crs4.it> | |
| 0 | 89 </help> |
|
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41ab1243e8f9
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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41ab1243e8f9
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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91 <citations> |
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41ab1243e8f9
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents:
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92 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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41ab1243e8f9
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
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93 </citations> |
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41ab1243e8f9
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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| 0 | 95 </tool> |