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annotate fastx_renamer.xml @ 1:defaa5ba1ee2 draft

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author devteam
date Tue, 13 Oct 2015 12:41:46 -0400
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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>
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7 <![CDATA[
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8 zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v
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9 #if $input.ext == "fastqsanger":
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10 -Q 33
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11 #end if
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12 ]]>
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13 </command>
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14
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15 <inputs>
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16 <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
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18 <param name="TYPE" type="select" label="Rename sequence identifiers to">
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19 <option value="SEQ">Nucleotides sequence</option>
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20 <option value="COUNT">Numeric Counter</option>
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21 </param>
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22 </inputs>
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23
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24 <outputs>
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25 <data format_source="input" name="output" metadata_source="input" />
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26 </outputs>
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27 <tests>
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28 </tests>
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29 <help>
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30 **What it does**
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31
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32 This tool renames the sequence identifiers in a FASTQ/A file.
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33
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34 .. class:: infomark
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35
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36 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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37
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38 --------
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39
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40 **Example**
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41
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42 The following Solexa-FASTQ file::
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43
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44 @CSHL_4_FC042GAMMII_2_1_517_596
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45 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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46 +CSHL_4_FC042GAMMII_2_1_517_596
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47 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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48
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49 Renamed to **nucleotides sequence**::
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51 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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52 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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53 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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54 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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56 Renamed to **numeric counter**::
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57
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58 @1
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59 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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60 +1
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61 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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62
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63 ------
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64
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65 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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66
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67 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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68 </help>
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69 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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70 </tool>