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1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
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2 <description></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>zcat -f $input | fastx_renamer -n $TYPE -o $output -v
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7 #if $input.ext == "fastqsanger":
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8 -Q 33
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9 #end if
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10 </command>
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11
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12 <inputs>
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13 <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
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14
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15 <param name="TYPE" type="select" label="Rename sequence identifiers to">
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16 <option value="SEQ">Nucleotides sequence</option>
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17 <option value="COUNT">Numeric Counter</option>
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18 </param>
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19 </inputs>
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20
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21 <outputs>
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22 <data format="input" name="output" metadata_source="input" />
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23 </outputs>
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24
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25 <help>
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26
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27 **What it does**
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28
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29 This tool renames the sequence identifiers in a FASTQ/A file.
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30
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31 .. class:: infomark
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32
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33 Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
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34
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35 --------
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36
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37 **Example**
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38
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39 The following Solexa-FASTQ file::
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40
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41 @CSHL_4_FC042GAMMII_2_1_517_596
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42 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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43 +CSHL_4_FC042GAMMII_2_1_517_596
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44 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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45
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46 Renamed to **nucleotides sequence**::
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47
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48 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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49 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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50 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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51 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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52
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53 Renamed to **numeric counter**::
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54
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55 @1
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56 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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57 +1
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58 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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59
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60 ------
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61
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62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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63
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64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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65 </help>
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66 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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67 </tool>
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