Mercurial > repos > iuc > codon_freq_from_bicodons

comparison codon_freq_from_bicodons.xml @ 0:cc5a776acd47 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
author iuc
date Mon, 11 Apr 2022 20:36:16 +0000
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1 <tool id="codon_freq_from_bicodons" name="Get Codon frequency" version="@TOOL_VERSION@" profile="20.05">
2 <description>from bicodons</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/>
8 <version_command>codon_freq_from_bicodons.py --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[
10 codon_freq_from_bicodons.py
11
12 --bicodons '$bicodons'
13
14 --taxid '$taxid'
15
16 --organelle '$organelle'
17
18 --out '$out'
19
20 --aa_out '$aa_out'
21
22 #if $write_log:
23 > '$log'
24 #end if
25 ]]></command>
26 <inputs>
27 <param argument="--bicodons" type="data" format="tabular" label="Bicondon rates input" help="Formatted like CoCoPUTs."/>
28 <param argument="--taxid" type="text" value="9606" label="Taxonomy ID of interest" help="9606 is Homo sapiens (human)"/>
29 <param argument="--organelle" type="text" value="genomic" label="Organelle of interest" help="genomic is default"/>
30 <param name="write_log" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Create log file"/>
31 </inputs>
32 <outputs>
33 <data name="out" format="tabular" label="Get Codon frequency on ${on_string}: codon counts"/>
34 <data name="aa_out" format="tabular" label="Get Codon frequency on ${on_string}: amino acid counts"/>
35 <data name="log" format="txt" label="Get Codon frequency on ${on_string}: log">
36 <filter>write_log</filter>
37 </data>
38 </outputs>
39 <tests>
40 <test expect_num_outputs="3">
41 <param name="bicodons" value="bicodon_out.tabular"/>
42 <param name="taxid" value="9606"/>
43 <param name="organelle" value="genomic"/>
44 <param name="write_log" value="true"/>
45 <output name="out" value="codon_freq_from_bicodon.tabular"/>
46 <output name="aa_out" value="aa_freq_from_bicodon.tabular"/>
47 <output name="log" value="codon_freq_from_bicodon_log.txt"/>
48 </test>
49 </tests>
50 <help><![CDATA[
51 Get Codon frequency from bicodons.
52
53 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).
54
55 Input row of interest is selected by the combination of the provided taxid and organelle.
56
57 Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
58
59 Example of CoCoPUTs style bicodon input, the majority of bicodons (codon pairs) have been removed in this example, for brevity:
60
61 +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
62 | Division | Assembly | Taxid | Species | Organelle | Translation Table | # CDS | # Codon Pairs | aaaaaa | aaaaac | aaaaag | aaaaat | ... |
63 +===========+===========+=======+==============+===========+===================+=======+===============+========+========+========+========+=====+
64 | custom | hg38 | 9606 | Homo sapiens | genomic | 1 | 4 | 859 | 0 | 0 | 0 | 1 | ... |
65 +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
66 ]]></help>
67 <expand macro="citations"/>
68 </tool>