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annotate fasta_nucleotide_changer.xml @ 2:1cabf6626797 draft

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author devteam
date Tue, 13 Oct 2015 12:39:17 -0400
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1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" >
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2 <description>converter</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 < '$input' | fasta_nucleotide_changer -$mode -v -o '$output'
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param format="fasta" name="input" type="data" label="Library to convert" />
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13
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14 <param name="mode" type="select" label="Convert">
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15 <option value="d">RNA to DNA (U to T)</option>
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16 <option value="r">DNA to RNA (T to U)</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data format_source="input" name="output" metadata_source="input" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="fasta_nuc_changer1.fasta" />
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25 <param name="mode" value="r" />
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26 <output name="output" ftype="fasta" file="fasta_nuc_change1.out" />
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27 </test>
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28 <test>
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29 <param name="input" value="fasta_nuc_changer2.fasta" />
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30 <param name="mode" value="d" />
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31 <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
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32 </test>
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33 </tests>
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34 <help>
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35 **What it does**
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36
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37 This tool converts RNA FASTA files to DNA (and vice-versa).
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38
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39 In **RNA-to-DNA** mode, U's are changed into T's.
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40
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41 In **DNA-to-RNA** mode, T's are changed into U's.
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42
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43 --------
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44
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45 **Example**
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46
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47 Input RNA FASTA file ( from Sanger's mirBase )::
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48
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49 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
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50 UGAGGUAGUAGGUUGUAUAGUU
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51 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
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52 UCCCUGAGACCUCAAGUGUGA
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53 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
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54 UGGAAUGUAAAGAAGUAUGUA
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55
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56 Output DNA FASTA file (with RNA-to-DNA mode)::
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57
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58 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7
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59 TGAGGTAGTAGGTTGTATAGTT
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60 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4
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61 TCCCTGAGACCTCAAGTGTGA
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62 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1
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63 TGGAATGTAAAGAAGTATGTA
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64
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65
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66 ------
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67
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68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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69
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70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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71 </help>
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72 </tool>