Mercurial > repos > mbernt > longorf
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author | mbernt |
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date | Mon, 07 Aug 2023 13:52:25 +0000 |
parents | 4952f1ece60b |
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<tool id="longORF" name="Obtain longest ORFs" version="0.3.0"> <description> in six-frame translations</description> <command><![CDATA[ python $__tool_directory__/getLongestORF.py $input $output_longestORF $output_ORFs ]]> </command> <inputs> <param name="input" format="fasta" type="data" label="sequences"/> </inputs> <outputs> <data name="output_longestORF" format="fasta"/> <data name="output_ORFs" format="tabular"/> </outputs> <tests> <test> <param name="input" value="test_input.fasta"/> <output name="output_longestORF" file="test_output.fasta"/> <output name="output_ORFs" file="test_output.tab"/> </test> </tests> <help><![CDATA[ **What it does** This tool identifies the longest Open Reading Frames within the six-frame translations of a set of sequences. **Input** It takes an amino acid fasta file with all open reading frames (+ and - strand) listed by the correspondng transcript. The tool is designed to process the output of the Galaxy tool "getorf" from the EMBOSS package. **Output** For each transcript, the respected longest ORF is identified and listed in fasta format. Furthermore, table with information about seqID, start, end, length, orientation, longest for all ORFs is given.]]> </help> </tool>