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annotate fastq_paired_end_joiner.xml @ 3:e659bd662045 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 06ff7f8972dcefaf52121c22ec82cf5d315adb3e-dirty
| author | devteam |
|---|---|
| date | Mon, 14 Dec 2015 16:03:18 -0500 |
| parents | ab37758348d0 |
| children | bce792b8e239 |
| rev | line source |
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e659bd662045
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 06ff7f8972dcefaf52121c22ec82cf5d315adb3e-dirty
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1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.1"> |
| 0 | 2 <description>on paired end reads</description> |
| 3 <requirements> | |
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e659bd662045
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 06ff7f8972dcefaf52121c22ec82cf5d315adb3e-dirty
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4 <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> |
| 0 | 5 </requirements> |
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e659bd662045
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 06ff7f8972dcefaf52121c22ec82cf5d315adb3e-dirty
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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' '${paste_sequence}'</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> | |
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3
e659bd662045
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner commit 06ff7f8972dcefaf52121c22ec82cf5d315adb3e-dirty
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14 <param name="paste_sequence" type="text" label="Bases to insert between joined reads" value="" help="Values are in Base-space and quality scores of maximal value will be used"/> |
| 0 | 15 </inputs> |
| 16 <outputs> | |
| 17 <data name="output_file" format="input" /> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" /> | |
| 22 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" /> | |
| 23 <output name="output_file" file="3.fastqsanger" /> | |
| 24 </test> | |
| 25 </tests> | |
| 26 <help> | |
| 27 **What it does** | |
| 28 | |
| 1 | 29 This tool joins paired end FASTQ reads from two separate files into a |
| 30 single read in one file. The join is performed using sequence | |
| 31 identifiers, allowing the two files to contain differing ordering. If | |
| 32 a sequence identifier does not appear in both files, it is excluded | |
| 33 from the output. | |
| 0 | 34 |
| 35 ----- | |
| 36 | |
| 37 **Input formats** | |
| 38 | |
| 1 | 39 Both old and new (from recent Illumina software) style FASTQ headers |
| 40 are supported. The following example uses the "old" style. | |
| 41 | |
| 0 | 42 Left-hand Read:: |
| 43 | |
| 44 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 | |
| 45 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC | |
| 46 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 | |
| 47 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh | |
| 48 | |
| 49 Right-hand Read:: | |
| 50 | |
| 51 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | |
| 52 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | |
| 53 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 | |
| 54 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | |
| 55 | |
| 56 ----- | |
| 57 | |
| 58 **Output** | |
| 59 | |
| 60 A multiple-fastq file, for example:: | |
| 61 | |
| 62 @HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
| 63 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA | |
| 64 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 | |
| 65 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR | |
| 66 | |
| 67 ------ | |
| 68 | |
| 1 | 69 **The "new" style** |
| 70 | |
| 71 Recent Illumina FASTQ headers are structured as follows:: | |
| 72 | |
| 73 @COORDS FLAGS | |
| 74 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y | |
| 75 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE | |
| 76 | |
| 77 where the whitespace character between COORDS and FLAGS can be either | |
| 78 a space or a tab. | |
| 0 | 79 |
| 1 | 80 ------ |
| 81 | |
| 82 **Credits** | |
| 0 | 83 |
| 1 | 84 This is an extended version (adds support for "new" style FASTQ headers) |
| 85 of D. Blankenberg's fastq joiner: | |
| 0 | 86 |
| 1 | 87 `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>`_ |
| 88 | |
| 89 New style header support added by Simone Leo <simone.leo@crs4.it> | |
| 0 | 90 </help> |
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91 |
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92 <citations> |
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93 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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94 </citations> |
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95 |
| 0 | 96 </tool> |