Mercurial > repos > devteam > fastq_to_tabular
annotate fastq_to_tabular.xml @ 1:7da7ddea4425 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:42:45 -0500 |
| parents | bc9269529e88 |
| children | ccf4e1d1fcbe |
| rev | line source |
|---|---|
| 0 | 1 <tool id="fastq_to_tabular" name="FASTQ to Tabular" version="1.1.0"> |
| 2 <description>converter</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">fastq_to_tabular.py '$input_file' '$output_file' $descr_columns '${input_file.extension[len( 'fastq' ):]}'</command> | |
| 7 <inputs> | |
| 8 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa" label="FASTQ file to convert" /> | |
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7da7ddea4425
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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9 <param name="descr_columns" type="integer" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column"> |
| 0 | 10 <validator type="in_range" min="1" /> |
| 11 </param> | |
| 12 </inputs> | |
| 13 <outputs> | |
| 14 <data name="output_file" format="tabular" /> | |
| 15 </outputs> | |
| 16 <tests> | |
| 17 <!-- basic test --> | |
| 18 <test> | |
| 19 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
| 20 <param name="descr_columns" value="1"/> | |
| 21 <output name="output_file" file="fastq_to_tabular_out_1.tabular" /> | |
| 22 </test> | |
| 23 <!-- color space test --> | |
| 24 <test> | |
| 25 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> | |
| 26 <param name="descr_columns" value="1"/> | |
| 27 <output name="output_file" file="fastq_to_tabular_out_2.tabular" /> | |
| 28 </test> | |
| 29 <!-- split title into columns --> | |
| 30 <test> | |
| 31 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
| 32 <param name="descr_columns" value="2"/> | |
| 33 <output name="output_file" file="fastq_to_tabular_out_3.tabular" /> | |
| 34 </test> | |
| 35 </tests> | |
| 36 <help> | |
| 37 | |
| 38 **What it does** | |
| 39 | |
| 40 This tool converts FASTQ sequencing reads to a Tabular file. | |
| 41 | |
| 42 It is conventional to take the first word of the FASTQ "@" title line as the identifier, and any remaining text to be a free form description. | |
| 43 It is therefore often useful to split this text into two columns in Galaxy (identifier and any description) by setting **How many columns to divide title string into?** to **2**. | |
| 44 In some cases the description can be usefully broken up into more columns -- see the examples . | |
| 45 | |
| 46 Tab characters, if present in the source FASTQ title, will be converted to spaces. | |
| 47 | |
| 48 ----- | |
| 49 | |
| 50 **Example** | |
| 51 | |
| 52 Consider the following two 454 reads in Sanger FASTQ format (using line wrapping for display, but do note not all tools will accept line wrapped FASTQ files):: | |
| 53 | |
| 54 @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] | |
| 55 tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT | |
| 56 GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact | |
| 57 ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca | |
| 58 tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta | |
| 59 aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn | |
| 60 +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] | |
| 61 FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF | |
| 62 D???:3104/76=:5...4.3,,,366////4<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===9 | |
| 63 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333 | |
| 64 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//, | |
| 65 ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7><;!!! | |
| 66 @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] | |
| 67 tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt | |
| 68 taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn | |
| 69 +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] | |
| 70 FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,, | |
| 71 ,11,,,.,,21777555513,..--1115758.//34488><<;;;;9944/!/4,,,57855!! | |
| 72 | |
| 73 By default this is converted into a 3 column tabular file, with the full FASTQ title used as column 1: | |
| 74 | |
| 75 =================================================================================================== ============== ============== | |
| 76 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!! | |
| 77 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!! | |
| 78 =================================================================================================== ============== ============== | |
| 79 | |
| 80 If you specified the title should be turned into 2 columns, you'd get 4 columns in total: | |
| 81 | |
| 82 ============== ==================================================================================== ============== ============== | |
| 83 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!! | |
| 84 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!! | |
| 85 ============== ==================================================================================== ============== ============== | |
| 86 | |
| 87 Similarly, for this example treating the title string as 7 columns makes sense: | |
| 88 | |
| 89 ============== ============ ========== =========== ============= ============== =================== ============== ============== | |
| 90 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!! | |
| 91 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!! | |
| 92 ============== ============ ========== =========== ============= ============== =================== ============== ============== | |
| 93 | |
| 94 Note the sequences and quality strings have been truncated for display purposes in the above tables. | |
| 95 | |
| 96 ------ | |
| 97 | |
| 98 </help> | |
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7da7ddea4425
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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99 |
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7da7ddea4425
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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100 <citations> |
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7da7ddea4425
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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101 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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7da7ddea4425
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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102 </citations> |
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7da7ddea4425
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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103 |
| 0 | 104 </tool> |