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annotate fastq_quality_converter.xml @ 1:253c7f4976e3 draft

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author devteam
date Tue, 13 Oct 2015 12:39:43 -0400
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1 <tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0">
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2 <description>(ASCII-Numeric)</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param format="fastq" name="input" type="data" label="Library to convert" />
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13
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14 <param name="QUAL_FORMAT" type="select" label="Desired output format">
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15 <option value="-a">ASCII (letters) quality scores</option>
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16 <option value="-n">Numeric quality scores</option>
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17 </param>
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18
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19 <param name="offset" type="select" label="FASTQ ASCII offset">
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20 <option value="33">33</option>
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21 <option selected="true" value="64">64</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data format="fastq" name="output" metadata_source="input" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <!-- ASCII to NUMERIC -->
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30 <param name="input" value="fastq_qual_conv1.fastq" />
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31 <param name="QUAL_FORMAT" value="Numeric quality scores" />
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32 <param name="offset" value="64" />
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33 <output name="output" file="fastq_qual_conv1.out" />
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34 </test>
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35 <test>
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36 <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
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37 <param name="input" value="fastq_qual_conv1.fastq" />
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38 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
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39 <param name="offset" value="64" />
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40 <output name="output" file="fastq_qual_conv1a.out" />
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41 </test>
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42 <test>
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43 <!-- NUMERIC to ASCII -->
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44 <param name="input" value="fastq_qual_conv2.fastq" />
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45 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
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46 <param name="offset" value="64" />
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47 <output name="output" file="fastq_qual_conv2.out" />
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48 </test>
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49 <test>
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50 <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
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51 <param name="input" value="fastq_qual_conv2.fastq" />
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52 <param name="QUAL_FORMAT" value="Numeric quality scores" />
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53 <param name="offset" value="64" />
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54 <output name="output" file="fastq_qual_conv2n.out" />
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55 </test>
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
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61
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62 .. class:: warningmark
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63
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64 Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
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65
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66 -----
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67
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68 FASTQ with Numeric quality scores::
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69
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70 @CSHL__2_FC042AGWWWXX:8:1:120:202
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71 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
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72 +CSHL__2_FC042AGWWWXX:8:1:120:202
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73 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8
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74 @CSHL__2_FC042AGWWWXX:8:1:103:1185
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75 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
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76 +CSHL__2_FC042AGWWWXX:8:1:103:1185
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77 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2
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80 FASTQ with ASCII quality scores::
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82 @CSHL__2_FC042AGWWWXX:8:1:120:202
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83 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
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84 +CSHL__2_FC042AGWWWXX:8:1:120:202
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85 hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH
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86 @CSHL__2_FC042AGWWWXX:8:1:103:1185
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87 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
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88 +CSHL__2_FC042AGWWWXX:8:1:103:1185
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89 hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B
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90
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91 ------
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92
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93 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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94
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95 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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96 </help>
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97 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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98 </tool>