Mercurial > repos > devteam > fasta_nucleotide_changer
annotate fasta_nucleotide_changer.xml @ 1:8789a0450ad4
Remove spurious version strings.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 26 Nov 2013 12:43:28 -0500 |
| parents | 399fe8a8ce37 |
| children | 1cabf6626797 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" > |
| 2 <description>converter</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
| 5 </requirements> | |
| 6 <command>zcat -f '$input' | fasta_nucleotide_changer -$mode -v -o $output</command> | |
| 7 <inputs> | |
|
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8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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8 <param format="fasta" name="input" type="data" label="Library to convert" /> |
| 0 | 9 |
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8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
10 <param name="mode" type="select" label="Convert"> |
| 0 | 11 <option value="d">RNA to DNA (U to T)</option> |
| 12 <option value="r">DNA to RNA (T to U)</option> | |
| 13 </param> | |
| 14 </inputs> | |
| 15 | |
| 16 <!-- | |
| 17 Functional tests with param value starting with - fail. | |
| 18 --> | |
| 19 <tests> | |
| 20 <test> | |
|
1
8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
21 <param name="input" value="fasta_nuc_changer1.fasta" /> |
|
8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
22 <param name="mode" value="r" /> |
|
8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
23 <output name="output" file="fasta_nuc_change1.out" /> |
| 0 | 24 </test> |
| 25 <test> | |
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1
8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
26 <param name="input" value="fasta_nuc_changer2.fasta" /> |
|
8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
27 <param name="mode" value="d" /> |
|
8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
28 <output name="output" file="fasta_nuc_change2.out" /> |
| 0 | 29 </test> |
| 30 </tests> | |
| 31 | |
| 32 <outputs> | |
|
1
8789a0450ad4
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
33 <data format="input" name="output" metadata_source="input" /> |
| 0 | 34 </outputs> |
| 35 | |
| 36 <help> | |
| 37 **What it does** | |
| 38 | |
| 39 This tool converts RNA FASTA files to DNA (and vice-versa). | |
| 40 | |
| 41 In **RNA-to-DNA** mode, U's are changed into T's. | |
| 42 | |
| 43 In **DNA-to-RNA** mode, T's are changed into U's. | |
| 44 | |
| 45 -------- | |
| 46 | |
| 47 **Example** | |
| 48 | |
| 49 Input RNA FASTA file ( from Sanger's mirBase ):: | |
| 50 | |
| 51 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 | |
| 52 UGAGGUAGUAGGUUGUAUAGUU | |
| 53 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 | |
| 54 UCCCUGAGACCUCAAGUGUGA | |
| 55 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 | |
| 56 UGGAAUGUAAAGAAGUAUGUA | |
| 57 | |
| 58 Output DNA FASTA file (with RNA-to-DNA mode):: | |
| 59 | |
| 60 >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 | |
| 61 TGAGGTAGTAGGTTGTATAGTT | |
| 62 >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 | |
| 63 TCCCTGAGACCTCAAGTGTGA | |
| 64 >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 | |
| 65 TGGAATGTAAAGAAGTATGTA | |
| 66 | |
| 67 | |
| 68 ------ | |
| 69 | |
| 70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 71 | |
| 72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
| 73 | |
| 74 </help> | |
| 75 </tool> |