annotate fastq_name_affixer.xml @ 25:5dba804e6884 draft

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author petr-novak
date Wed, 02 Aug 2023 12:42:08 +0000
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id="names_affixer" name="FASTQ Read name affixer" version="1.0.0.3">
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2 <description>Tool appending suffix and prefix to sequences names</description>
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3 <required_files>
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4 <include type="literal" path="name_affixer.py"/>
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5 </required_files>
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6 <command>
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7 ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n
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8 $nspace > $output
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9 </command>
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11 <inputs>
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12 <param format="fastq" type="data" name="input" label="Choose your FASTQ file"/>
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13 <param name="prefix" type="text" size="10" value="" label="Prefix"
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14 help="Enter prefix which will be added to all sequences names"/>
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15 <param name="suffix" type="text" size="10" value="" label="Suffix"
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16 help="Enter suffix which will be added to all sequences names"/>
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17 <param name="nspace" type="integer" size="10" value="0" min="0" max="1000"
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18 label="Number of spaces in sequence name to ignore"
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19 help="Sequence name is a string before the first space. If you want name to include spaces in name, enter positive integer. All other characters beyond ignored spaces are omitted"/>
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20 </inputs>
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23 <outputs>
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24 <data format="fastq" name="output"
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25 label="FASTQ dataset ${input.hid} with modified sequence names"/>
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26 </outputs>
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27
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28 <help>
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29 **What is does**
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31 Tool for appending prefix and suffix to sequences names in fastq formated
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32 sequences.
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34 **Example**
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35
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36 The following Solexa-FASTQ file:
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37
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38 ::
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40 @CSHL_4_FC042GAMMII_2_1_517_596
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41 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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42 +CSHL_4_FC042GAMMII_2_1_517_596
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43 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24
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44 24 9 24 9 40 10 10 15 40
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45
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46 is renamed to:
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47
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48 ::
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50 @prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
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51 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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52 +prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
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53 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24
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54 24 9 24 9 40 10 10 15 40
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55
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56 different format:
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59 ::
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61 @HISEQ1:92:c0190acxx:8:1101:1252:2230 2:N:0:CGATGT
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62 AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
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63 +
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64 CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
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66 is renamed to:
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68 ::
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70 @prefixHISEQ1:92:c0190acxx:8:1101:1252:2230suffix
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71 AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
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72 +
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73 CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
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74
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75 note that string after first space is omitted!
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77 Because sequence names sometimes containg spaces which delimit the actual name. By
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78 default, anything after spaces is
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79 excluded from sequences name. In example sequence:
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81 ::
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83 @SRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1
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84 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
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85 +
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86 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
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88 when **Number of spaces in name to ignore** is set to 0 (default) the output will
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89 be:
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91 ::
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93 @prefixSRR352150.23846180suffix
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94 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
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95 +
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96 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
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97
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98 If you want to keep spaces the setting **Number of spaces in name to ignore** to 1
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99 will yield
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101 ::
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103 @prefixSRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1suffix
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104 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
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105 +
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106 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
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107
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108
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109 </help>
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110 </tool>