Mercurial > repos > mbernt > longorf
diff longORF.xml @ 0:ec898924d8c7 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
author | mbernt |
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date | Wed, 20 Jun 2018 11:02:06 -0400 |
parents | |
children | 4952f1ece60b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/longORF.xml Wed Jun 20 11:02:06 2018 -0400 @@ -0,0 +1,35 @@ +<tool id="longORF" name="Obtain longest ORFs" version="0.1.0"> + <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>