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1 <tool id="cshl_fastq_quality_converter" name="Quality format converter">
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2 <description>(ASCII-Numeric)</description>
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3 <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output</command>
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4 <inputs>
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5 <param format="fastqsolexa" name="input" type="data" label="Library to convert" />
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6
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7 <param name="QUAL_FORMAT" type="select" label="Desired output format">
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8 <option value="-a">ASCII (letters) quality scores</option>
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9 <option value="-n">Numeric quality scores</option>
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10 </param>
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11 </inputs>
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12
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13 <tests>
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14 <test>
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15 <!-- ASCII to NUMERIC -->
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16 <param name="input" value="fastq_qual_conv1.fastq" />
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17 <param name="QUAL_FORMAT" value="Numeric quality scores" />
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18 <output name="output" file="fastq_qual_conv1.out" />
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19 </test>
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20 <test>
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21 <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
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22 <param name="input" value="fastq_qual_conv1.fastq" />
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23 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
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24 <output name="output" file="fastq_qual_conv1a.out" />
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25 </test>
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26 <test>
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27 <!-- NUMERIC to ASCII -->
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28 <param name="input" value="fastq_qual_conv2.fastq" />
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29 <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
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30 <output name="output" file="fastq_qual_conv2.out" />
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31 </test>
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32 <test>
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33 <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
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34 <param name="input" value="fastq_qual_conv2.fastq" />
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35 <param name="QUAL_FORMAT" value="Numeric quality scores" />
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36 <output name="output" file="fastq_qual_conv2n.out" />
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37 </test>
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38 </tests>
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39
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40 <outputs>
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41 <data format="fastqsolexa" name="output" metadata_source="input" />
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42 </outputs>
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43 <help>
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44
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45 **What it does**
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46
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47 Converts a solexa FASTQ file to/from numeric or ASCII quality format.
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48
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49 .. class:: warningmark
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50
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51 Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
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52
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53
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54 -----
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55
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56 FASTQ with Numeric quality scores::
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57
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58 @CSHL__2_FC042AGWWWXX:8:1:120:202
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59 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC
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60 +CSHL__2_FC042AGWWWXX:8:1:120:202
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61 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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62 @CSHL__2_FC042AGWWWXX:8:1:103:1185
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63 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC
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64 +CSHL__2_FC042AGWWWXX:8:1:103:1185
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65 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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66
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67
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68 FASTQ with ASCII 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 hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH
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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 hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B
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78
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79
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80 </help>
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81 </tool>
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82 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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