annotate fastq_name_affixer.xml @ 7:89c5ba120b21 draft

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author petr-novak
date Mon, 02 Dec 2019 08:41:43 -0500
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1 <tool id="names_affixer" name="FASTQ Read name affixer" version="1.0.0">
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2 <description> Tool appending suffix and prefix to sequences names </description>
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3 <command interpreter="python">
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4 ${__tool_directory__}/name_affixer.py -f $input -p "$prefix" -s "$suffix" -n $nspace > $output
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5 </command>
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6
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7 <inputs>
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8 <param format="fastq" type="data" name="input" label="Choose your fastq file" />
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9 <param name="prefix" type="text" size="10" value="" label="Prefix" help="Enter prefix which will be added to all sequences names" />
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10 <param name="suffix" type="text" size="10" value="" label="Suffix" help="Enter suffix which will be added to all sequences names"/>
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11 <param name="nspace" type="integer" size="10" value="0" min="0" max="1000" label="Number of spaces in name to ignore" 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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12 </inputs>
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15 <outputs>
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16 <data format="fastq" name="output" label="fastq dataset ${input.hid} with modified sequence names" />
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17 </outputs>
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18
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19 <help>
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20 **What is does**
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21
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22 Tool for appending prefix and suffix to sequences names in fastq formated sequences.
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23
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24 **Example**
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25
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26 The following Solexa-FASTQ file:
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27
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28 ::
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29
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30 @CSHL_4_FC042GAMMII_2_1_517_596
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31 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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32 +CSHL_4_FC042GAMMII_2_1_517_596
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33 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 24 9 24 9 40 10 10 15 40
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34
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35 is renamed to:
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36
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37 ::
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38
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39 @prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
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40 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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41 +prefixCSHL_4_FC042GAMMII_2_1_517_596suffix
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42 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 24 9 24 9 40 10 10 15 40
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43
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44 different format:
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47 ::
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48
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49 @HISEQ1:92:c0190acxx:8:1101:1252:2230 2:N:0:CGATGT
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50 AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
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51 +
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52 CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
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54 is renamed to:
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56 ::
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57
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58 @prefixHISEQ1:92:c0190acxx:8:1101:1252:2230suffix
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59 AGAGGAAAAAACATAGTTCTTGTCTAAAAAAATCCCTTGAAAAAGGGCAGATGTATAGAAATAGAAAATTTCAAAGAAAAACTCTCTACAAATGGAAGAGA
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60 +
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61 CCCFFFFFHHHHHJJJJIJJJJJJJJJJJJJJJIJJJJJIIJJJJJJGIJIJIHHHHHHHHFFFFFFDEEEEEDCDDDDDDDCCDDDEDDDDD>CCCCB@9
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62
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63 note that string after first space is omitted!
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64
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65 Because sequence names sometimes containg spaces which delimit the actual name. By default, anything after spaces is
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66 excluded from sequences name. In example sequence:
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67
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68 ::
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69
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70 @SRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1
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71 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
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72 +
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73 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
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74
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75 when **Number of spaces in name to ignore** is set to 0 (default) the output will be:
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77 ::
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78
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79 @prefixSRR352150.23846180suffix
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80 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
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81 +
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82 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
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83
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84 If you want to keep spaces the setting **Number of spaces in name to ignore** to 1 will yield
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85
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86 ::
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87
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88 @prefixSRR352150.23846180 HWUSI-EAS1786:7:119:15910:19280/1suffix
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89 CTGGATTCTATACCTTTGGCAACTACTTCTTGGTTGATCAGGAAATTAACACTAGTAGTTTAGGCAATTTGGAATGGTGCCAAAGATGTATAGAACTTTC
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90 +
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91 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGIIIHIIIIIFIIIIIIHDHBBIHFIHIIBHHDDHIFHIHIIIHIHGGDFDEI@EGEGFGFEFB@ECG
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92
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93
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94 </help>
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95 </tool>