[2] | 1 | <tool id="cshl_fasta_nucleotides_changer" name="RNA/DNA" > |
---|
| 2 | <description>converter</description> |
---|
| 3 | <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
|
---|
| 4 | <command>zcat -f '$input' | fasta_nucleotide_changer $mode -v -o $output</command> |
---|
| 5 | <inputs> |
---|
| 6 | <param format="fasta" name="input" type="data" label="Library to convert" /> |
---|
| 7 | |
---|
| 8 | <param name="mode" type="select" label="Convert"> |
---|
| 9 | <option value="-d">RNA to DNA (U to T)</option> |
---|
| 10 | <option value="-r">DNA to RNA (T to U)</option> |
---|
| 11 | </param> |
---|
| 12 | </inputs> |
---|
| 13 | |
---|
| 14 | <!-- |
---|
| 15 | Functional tests with param value starting with - fail. |
---|
| 16 | <tests> |
---|
| 17 | <test> |
---|
| 18 | <param name="input" value="fasta_nuc_changer1.fasta" /> |
---|
| 19 | <param name="mode" value="-r" /> |
---|
| 20 | <output name="output" file="fasta_nuc_change1.out" /> |
---|
| 21 | </test> |
---|
| 22 | <test> |
---|
| 23 | <param name="input" value="fasta_nuc_changer2.fasta" /> |
---|
| 24 | <param name="mode" value="-d" /> |
---|
| 25 | <output name="output" file="fasta_nuc_change2.out" /> |
---|
| 26 | </test> |
---|
| 27 | </tests> |
---|
| 28 | --> |
---|
| 29 | |
---|
| 30 | <outputs> |
---|
| 31 | <data format="input" name="output" metadata_source="input" /> |
---|
| 32 | </outputs> |
---|
| 33 | |
---|
| 34 | <help> |
---|
| 35 | **What it does** |
---|
| 36 | |
---|
| 37 | This tool converts RNA FASTA files to DNA (and vice-versa). |
---|
| 38 | |
---|
| 39 | In **RNA-to-DNA** mode, U's are changed into T's. |
---|
| 40 | |
---|
| 41 | In **DNA-to-RNA** mode, T's are changed into U's. |
---|
| 42 | |
---|
| 43 | -------- |
---|
| 44 | |
---|
| 45 | **Example** |
---|
| 46 | |
---|
| 47 | Input RNA FASTA file ( from Sanger's mirBase ):: |
---|
| 48 | |
---|
| 49 | >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 |
---|
| 50 | UGAGGUAGUAGGUUGUAUAGUU |
---|
| 51 | >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 |
---|
| 52 | UCCCUGAGACCUCAAGUGUGA |
---|
| 53 | >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 |
---|
| 54 | UGGAAUGUAAAGAAGUAUGUA |
---|
| 55 | |
---|
| 56 | Output DNA FASTA file (with RNA-to-DNA mode):: |
---|
| 57 | |
---|
| 58 | >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 |
---|
| 59 | TGAGGTAGTAGGTTGTATAGTT |
---|
| 60 | >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 |
---|
| 61 | TCCCTGAGACCTCAAGTGTGA |
---|
| 62 | >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 |
---|
| 63 | TGGAATGTAAAGAAGTATGTA |
---|
| 64 | |
---|
| 65 | </help> |
---|
| 66 | </tool> |
---|