view codon_freq_from_bicodons.xml @ 0:60e1f1caedad draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"

<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>