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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
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2 <description>converter</description>
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3 <command>
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4 cat '$input' |
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5 fastq_to_fasta
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6 #if $input.ext == "fastqsanger":
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7 -Q 33
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8 #elif $input.ext == "fastq":
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9 -Q 64
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10 #end if
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11 $SKIPN $RENAMESEQ -o '$output' -v
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12 </command>
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13 <inputs>
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14 <param format="fastq,fastqsanger" name="input" type="data" label="FASTQ Library to convert" />
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15
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16 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
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17 <option value="">yes</option>
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18 <option value="-n">no</option>
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19 </param>
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20
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21 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
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22 <option value="-r">yes</option>
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23 <option value="">no</option>
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24 </param>
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25
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26 </inputs>
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27
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28 <tests>
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29 <test>
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30 <!-- FASTQ-To-FASTA, keep N, don't rename -->
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31 <param name="input" value="fastq_to_fasta1.fastq" />
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32 <param name="SKIPN" value=""/>
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33 <param name="RENAMESEQ" value=""/>
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34 <output name="output" file="fastq_to_fasta1a.out" />
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35 </test>
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36 <test>
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37 <!-- FASTQ-To-FASTA, discard N, rename -->
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38 <param name="input" value="fastq_to_fasta1.fastq" />
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39 <param name="SKIPN" value="no"/>
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40 <param name="RENAMESEQ" value="yes"/>
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41 <output name="output" file="fastq_to_fasta1b.out" />
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42 </test>
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43 </tests>
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44
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45 <outputs>
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46 <data format="fasta" name="output" metadata_source="input"
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47 />
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48 </outputs>
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49
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50 <help>
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51
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52 **What it does**
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53
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54 This tool converts data from Solexa format to FASTA format (scroll down for format description).
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55
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56 --------
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57
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58 **Example**
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59
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60 The following data in Solexa-FASTQ format::
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61
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62 @CSHL_4_FC042GAMMII_2_1_517_596
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63 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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64 +CSHL_4_FC042GAMMII_2_1_517_596
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65 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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66
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67 Will be converted to FASTA (with 'rename sequence names' = NO)::
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68
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69 >CSHL_4_FC042GAMMII_2_1_517_596
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70 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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71
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72 Will be converted to FASTA (with 'rename sequence names' = YES)::
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73
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74 >1
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75 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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76
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77 ------
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78
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79 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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80
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81 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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82 </help>
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83 </tool>
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84 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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