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annotate fasta_nucleotide_changer.xml @ 5:ec0b5076173a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:28:49 -0500
parents 091ca73f5804
children f773e98b26cf
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091ca73f5804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
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1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.2" name="RNA/DNA" >
2
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2 <description>converter</description>
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3 <macros>
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4 <import>macros.xml</import>
cc9a18dd41c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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5 </macros>
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6 <expand macro="requirements" />
cc9a18dd41c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fasta_nucleotide_changer
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9 -$mode
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10 -v
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ec0b5076173a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
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11 @GZIP@ > '$output'
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cc9a18dd41c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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12 ]]></command>
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13 <inputs>
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cc9a18dd41c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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14 <expand macro="fasta_input" />
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15
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16 <param name="mode" type="select" label="Convert">
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17 <option value="d">RNA to DNA (U to T)</option>
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18 <option value="r">DNA to RNA (T to U)</option>
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19 </param>
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20 </inputs>
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21 <outputs>
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cc9a18dd41c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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22 <data name="output" format_source="input" metadata_source="input" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="fasta_nuc_changer1.fasta" />
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27 <param name="mode" value="r" />
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28 <output name="output" ftype="fasta" file="fasta_nuc_change1.out" />
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29 </test>
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30 <test>
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31 <param name="input" value="fasta_nuc_changer2.fasta" />
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32 <param name="mode" value="d" />
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33 <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
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34 </test>
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35 </tests>
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cc9a18dd41c9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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36 <help><![CDATA[
0
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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
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70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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71
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72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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73 ]]></help>
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74 <expand macro="citations" />
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75 </tool>