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annotate fastq_to_tabular.xml @ 4:672ad99bbfe4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_to_tabular commit 31edb920789fbd080260f853bc856be72fa7cfa8"
author devteam
date Fri, 01 Nov 2019 13:20:52 -0400
parents a63d1aa8e829
children c9031442b526
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1 <tool id="fastq_to_tabular" name="FASTQ to Tabular" version="1.1.1">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
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5 </requirements>
4
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6 <edam_topics>
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7 <edam_topic>topic_0622</edam_topic>
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8 </edam_topics>
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9 <edam_operations>
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10 <edam_operation>operation_0233</edam_operation>
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11 </edam_operations>
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12 <command><![CDATA[
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13 gx-fastq-to-tabular '$input_file' '$output_file' $descr_columns '${input_file.extension[len('fastq'):]}'
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14 ]]></command>
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15 <inputs>
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16 <param name="input_file" type="data" format="fastqsanger,fastqcssanger,fastqillumina,fastqsolexa,fastqsanger.gz,fastqcssanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqsanger.bz2,fastqcssanger.bz2,fastqillumina.bz2,fastqsolexa.bz2" label="FASTQ file to convert" />
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17 <param name="descr_columns" type="integer" min="1" 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" />
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18 </inputs>
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19 <outputs>
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20 <data name="output_file" format="tabular" />
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21 </outputs>
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22 <tests>
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23 <!-- basic test -->
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24 <test>
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25 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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26 <param name="descr_columns" value="1"/>
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27 <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
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28 </test>
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29 <!-- compression test -->
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30 <test>
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31 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" />
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32 <param name="descr_columns" value="1"/>
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33 <output name="output_file" file="fastq_to_tabular_out_1.tabular" />
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34 </test>
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35 <!-- color space test -->
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36 <test>
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37 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
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38 <param name="descr_columns" value="1"/>
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39 <output name="output_file" file="fastq_to_tabular_out_2.tabular" />
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40 </test>
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41 <!-- split title into columns -->
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42 <test>
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43 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
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44 <param name="descr_columns" value="2"/>
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45 <output name="output_file" file="fastq_to_tabular_out_3.tabular" />
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46 </test>
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47 </tests>
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48 <help><![CDATA[
0
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49 **What it does**
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50
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51 This tool converts FASTQ sequencing reads to a Tabular file.
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52
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53 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.
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54 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**.
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55 In some cases the description can be usefully broken up into more columns -- see the examples .
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56
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57 Tab characters, if present in the source FASTQ title, will be converted to spaces.
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58
3
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59 -----
0
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60
e018cfd2dc02 Imported from capsule None
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61 **Example**
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62
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63 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)::
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64
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65 @FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
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66 tcagTTAAGATGGGATAATATCCTCAGATTGCGTGATGAACTTTGTTCTGGTGGAGGAGAAGGAAGTGCATTCGACGTAT
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67 GCCCGTTTGTCGATATTTGtatttaaagtaatccgtcacaaatcagtgacataaatattatttagatttcgggagcaact
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68 ttatttattccacaagcaggtttaaattttaaatttaaattattgcagaagactttaaattaacctcgttgtcggagtca
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69 tttgttcggttattggtcgaaagtaaccncgggaagtgccgaaaactaacaaacaaaagaagatagtgaaattttaatta
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70 aaanaaatagccaaacgtaactaactaaaacggacccgtcgaggaactgccaacggacgacacagggagtagnnn
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71 +FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95]
0
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72 FFFDDDDDDDA666?688FFHGGIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIGHGFFFFF====DFFFFFFFFFFFFFF
3
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73 D???:3104/76=:5...4.3,,,366////4<ABBAAA=CCFDDDDDDDD:666CDFFFF=<ABA=;:333111<===9
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74 9;B889FFFFFFDDBDBDDD=8844231..,,,-,,,,,,,,1133..---17111,,,,,22555131121.--.,333
0
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75 11,.,,3--,,.,,--,3511123..--!,,,,--,----9,,,,8=,,-,,,-,,,,---26:9:5-..1,,,,11//,
3
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76 ,,,!,,1917--,,,,-3.,--,,17,,,,---+11113.030000,,,044400036;96662.//;7><;!!!
0
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77 @FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
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78 tcagCCAGCAATTCCGACTTAATTGTTCTTCTTCCATCATTCATCTCGACTAACAGTTCTACGATTAATGAGTTTGGCtt
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79 taatttgttgttcattattgtcacaattacactactgagactgccaaggcacncagggataggnn
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80 +FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74]
3
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81 FFFFFFFFFDDDDFFFFGFDDDDBAAAAA=<4444@@B=555:BBBBB@@?8:8<?<89898<84442;==3,,,514,,
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82 ,11,,,.,,21777555513,..--1115758.//34488><<;;;;9944/!/4,,,57855!!
0
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83
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84 By default this is converted into a 3 column tabular file, with the full FASTQ title used as column 1:
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85
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86 =================================================================================================== ============== ==============
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87 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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88 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
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89 =================================================================================================== ============== ==============
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90
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91 If you specified the title should be turned into 2 columns, you'd get 4 columns in total:
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92
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93 ============== ==================================================================================== ============== ==============
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94 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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95 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
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96 ============== ==================================================================================== ============== ==============
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97
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98 Similarly, for this example treating the title string as 7 columns makes sense:
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99
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100 ============== ============ ========== =========== ============= ============== =================== ============== ==============
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101 FSRRS4401BE7HA [length=395] [gc=36.46] [flows=800] [phred_min=0] [phred_max=40] [trimmed_length=95] tcagTTAA...nnn FFFDDDDD...!!!
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102 FSRRS4401BRRTC [length=145] [gc=38.62] [flows=800] [phred_min=0] [phred_max=38] [trimmed_length=74] tcagCCAG...gnn FFFFFFFF...5!!
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103 ============== ============ ========== =========== ============= ============== =================== ============== ==============
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104
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105 Note the sequences and quality strings have been truncated for display purposes in the above tables.
3
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106 ]]></help>
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107 <citations>
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108 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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109 </citations>
0
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110 </tool>