Mercurial > repos > iuc > codon_freq_from_bicodons
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
author | iuc |
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date | Mon, 11 Apr 2022 20:36:16 +0000 |
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<tool id="codon_freq_from_bicodons" name="Get Codon frequency" version="@TOOL_VERSION@" profile="20.05"> <description>from bicodons</description> <macros> <import>macros.xml</import> </macros> <expand macro="edam_ontology"/> <expand macro="requirements"/> <version_command>codon_freq_from_bicodons.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ codon_freq_from_bicodons.py --bicodons '$bicodons' --taxid '$taxid' --organelle '$organelle' --out '$out' --aa_out '$aa_out' #if $write_log: > '$log' #end if ]]></command> <inputs> <param argument="--bicodons" type="data" format="tabular" label="Bicondon rates input" help="Formatted like CoCoPUTs."/> <param argument="--taxid" type="text" value="9606" label="Taxonomy ID of interest" help="9606 is Homo sapiens (human)"/> <param argument="--organelle" type="text" value="genomic" label="Organelle of interest" help="genomic is default"/> <param name="write_log" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Create log file"/> </inputs> <outputs> <data name="out" format="tabular" label="Get Codon frequency on ${on_string}: codon counts"/> <data name="aa_out" format="tabular" label="Get Codon frequency on ${on_string}: amino acid counts"/> <data name="log" format="txt" label="Get Codon frequency on ${on_string}: log"> <filter>write_log</filter> </data> </outputs> <tests> <test expect_num_outputs="3"> <param name="bicodons" value="bicodon_out.tabular"/> <param name="taxid" value="9606"/> <param name="organelle" value="genomic"/> <param name="write_log" value="true"/> <output name="out" value="codon_freq_from_bicodon.tabular"/> <output name="aa_out" value="aa_freq_from_bicodon.tabular"/> <output name="log" value="codon_freq_from_bicodon_log.txt"/> </test> </tests> <help><![CDATA[ Get Codon frequency from bicodons. Input format should match that provided by CoCoPUTs (https://dnahive.fda.gov/dna.cgi?cmd=codon_usage&id=537&mode=cocoputs; e.g. https://dnahive.fda.gov/dna.cgi?cmd=objFile&ids=537&filename=Refseq_Bicod.tsv&raw=1). Input row of interest is selected by the combination of the provided taxid and organelle. Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi). Example of CoCoPUTs style bicodon input, the majority of bicodons (codon pairs) have been removed in this example, for brevity: +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+ | Division | Assembly | Taxid | Species | Organelle | Translation Table | # CDS | # Codon Pairs | aaaaaa | aaaaac | aaaaag | aaaaat | ... | +===========+===========+=======+==============+===========+===================+=======+===============+========+========+========+========+=====+ | custom | hg38 | 9606 | Homo sapiens | genomic | 1 | 4 | 859 | 0 | 0 | 0 | 1 | ... | +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+ ]]></help> <expand macro="citations"/> </tool>