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1 <tool id="cshl_fasta_nucleotides_changer" name="RNA/DNA" >
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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 fasta_nucleotide_changer $mode -v -o '$output'</command>
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6 <inputs>
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7 <param format="fasta" name="input" type="data" label="Library to convert" />
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8
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9 <param name="mode" type="select" label="Convert">
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10 <option value="-d">RNA to DNA (U to T)</option>
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11 <option value="-r">DNA to RNA (T to U)</option>
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12 </param>
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13 </inputs>
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14
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15 <tests>
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16 <test>
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17 <!-- DNA-to-RNA -->
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18 <param name="input" value="fasta_nuc_changer1.fasta" />
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19 <param name="mode" value="DNA to RNA (T to U)" />
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20 <output name="output" file="fasta_nuc_changer1.out" />
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21 </test>
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22 <test>
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23 <!-- RNA-to-DNA -->
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24 <param name="input" value="fasta_nuc_changer2.fasta" />
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25 <param name="mode" value="RNA to DNA (U to T)" />
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26 <output name="output" file="fasta_nuc_changer2.out" />
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27 </test>
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28 </tests>
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29
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30
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31 <outputs>
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32 <data format="input" name="output" metadata_source="input"
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33 />
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34 </outputs>
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35
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36 <help>
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37 **What it does**
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38
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39 This tool converts RNA FASTA files to DNA (and vice-versa).
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40
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41 In **RNA-to-DNA** mode, U's are changed into T's.
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42
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43 In **DNA-to-RNA** mode, T's are changed into U's.
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44
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45 --------
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46
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47 **Example**
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48
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49 Input RNA FASTA file ( from Sanger's mirBase )::
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50
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51 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
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52 UGAGGUAGUAGGUUGUAUAGUU
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53 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
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54 UCCCUGAGACCUCAAGUGUGA
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55 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
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56 UGGAAUGUAAAGAAGUAUGUA
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57
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58 Output DNA FASTA file (with RNA-to-DNA mode)::
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59
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60 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
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61 TGAGGTAGTAGGTTGTATAGTT
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62 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
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63 TCCCTGAGACCTCAAGTGTGA
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64 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
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65 TGGAATGTAAAGAAGTATGTA
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66
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67 ------
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68
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69 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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70
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71 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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72 </help>
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73 </tool>
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74 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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