Mercurial > repos > idot > fastx_toolkit2
view fasta_nucleotide_changer.xml @ 1:e7c65e398bdd draft default tip
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author | idot |
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date | Wed, 10 Jul 2013 06:16:21 -0400 |
parents | 78a7d28f2a15 |
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<tool id="cshl_fasta_nucleotides_changer" name="RNA/DNA" > <description>converter</description> <command> cat '$input' | fasta_nucleotide_changer $mode -v -o '$output'</command> <inputs> <param format="fasta" name="input" type="data" label="Library to convert" /> <param name="mode" type="select" label="Convert"> <option value="-d">RNA to DNA (U to T)</option> <option value="-r">DNA to RNA (T to U)</option> </param> </inputs> <tests> <test> <!-- DNA-to-RNA --> <param name="input" value="fasta_nuc_changer1.fasta" /> <param name="mode" value="DNA to RNA (T to U)" /> <output name="output" file="fasta_nuc_changer1.out" /> </test> <test> <!-- RNA-to-DNA --> <param name="input" value="fasta_nuc_changer2.fasta" /> <param name="mode" value="RNA to DNA (U to T)" /> <output name="output" file="fasta_nuc_changer2.out" /> </test> </tests> <outputs> <data format="input" name="output" metadata_source="input" /> </outputs> <help> **What it does** This tool converts RNA FASTA files to DNA (and vice-versa). In **RNA-to-DNA** mode, U's are changed into T's. In **DNA-to-RNA** mode, T's are changed into U's. -------- **Example** Input RNA FASTA file ( from Sanger's mirBase ):: >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 UGAGGUAGUAGGUUGUAUAGUU >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 UCCCUGAGACCUCAAGUGUGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 UGGAAUGUAAAGAAGUAUGUA Output DNA FASTA file (with RNA-to-DNA mode):: >cel-let-7 MIMAT0000001 Caenorhabditis elegans let-7 TGAGGTAGTAGGTTGTATAGTT >cel-lin-4 MIMAT0000002 Caenorhabditis elegans lin-4 TCCCTGAGACCTCAAGTGTGA >cel-miR-1 MIMAT0000003 Caenorhabditis elegans miR-1 TGGAATGTAAAGAAGTATGTA ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool> <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->