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comparison bicodon_counts_from_fasta.xml @ 0:4fece4418832 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 20:35:02 +0000
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1 <tool id="bicodon_counts_from_fasta" name="Get Codon and Bicodon frequency" version="@TOOL_VERSION@" profile="20.05">
2 <description>from FASTA files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/>
8 <version_command>bicodon_counts_from_fasta.py --version</version_command>
9 <command detect_errors="exit_code"><![CDATA[
10 bicodon_counts_from_fasta.py
11 #if $ref.ref_source == 'cached':
12 --seq '${ref.ref_loc.fields.path}'
13 #elif $ref.ref_source == 'history':
14 --seq '${ref.ref_file}'
15 #end if
16
17 --taxid '$taxid'
18
19 --organelle '$organelle'
20
21 --division '$division'
22
23 --assembly '$assembly'
24
25 --species '$species'
26
27 --translation_table '$translation_table'
28
29 --codon_out '$codon_out'
30
31 --bicodon_out '$bicodon_out'
32 ]]></command>
33 <inputs>
34 <conditional name="ref">
35 <param name="ref_source" type="select" label="Source for Sequence Data">
36 <option value="cached">Locally cached FASTA</option>
37 <option value="history" selected="True">History dataset FASTA</option>
38 </param>
39 <when value="cached">
40 <param argument="--seq" name="ref_loc" type="select" label="Select FASTA nucleotide sequences">
41 <options from_data_table="all_fasta"/>
42 </param>
43 </when>
44 <when value="history">
45 <param argument="--seq" name="ref_file" type="data" format="fasta" label="FASTA nucleotide sequences"/>
46 </when>
47 </conditional>
48 <param argument="--taxid" type="text" value="9606" label="Taxonomy ID to list in output" help="9606 is Homo sapiens (human)"/>
49 <param argument="--organelle" type="text" value="genomic" label="Organelle to list in output" help="genomic is default"/>
50 <param argument="--division" type="text" value="custom" label="Division to list in output" help="custom is default"/>
51 <param argument="--assembly" type="text" value="hg38" label="Assembly to list in output" help="hg38 is default"/>
52 <param argument="--species" type="text" value="Homo sapiens" label="Species to list in output" help="Homo sapiens is default"/>
53 <expand macro="translation_table_select_parameter"/>
54 </inputs>
55 <outputs>
56 <data name="codon_out" format="tabular" label="Get Codon and Bicodon frequency on ${on_string}: #if $ref.ref_source == 'cached' then $ref.ref_loc.fields.name else $ref.ref_file.name# codon usage output"/>
57 <data name="bicodon_out" format="tabular" label="Get Codon and Bicodon frequency on ${on_string}: #if $ref.ref_source == 'cached' then $ref.ref_loc.fields.name else $ref.ref_file.name# bicodon usage"/>
58 </outputs>
59 <tests>
60 <test>
61 <conditional name="ref">
62 <param name="ref_source" value="history"/>
63 <param name="ref_file" value="naltorfs_fasta_out.fasta" dbkey="hg38" ftype="fasta"/>
64 </conditional>
65 <param name="taxid" value="9606"/>
66 <param name="organelle" value="genomic"/>
67 <param name="division" value="custom"/>
68 <param name="assembly" value="hg38"/>
69 <param name="species" value="Homo sapiens"/>
70 <param name="translation_table" value="1"/>
71 <output name="codon_out" value="codon_out.tabular"/>
72 <output name="bicodon_out" value="bicodon_out.tabular"/>
73 </test>
74 </tests>
75 <help><![CDATA[
76 Calculate Codon and Bicodon (Codon Pair) usage frequency from FASTA files.
77
78 Output is designed to mimic that from 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).
79
80 Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
81
82 Example of CoCoPUTs style codon output, the majority of codons have been removed in this example, for brevity:
83
84 +-----------+-----------+-------+--------------+-----------+-------------------+-------+----------+-----+-----+-----+-----+-----+
85 | Division | Assembly | Taxid | Species | Organelle | Translation Table | # CDS | # Codons | aaa | aac | aag | aat | ... |
86 +===========+===========+=======+==============+===========+===================+=======+==========+=====+=====+=====+=====+=====+
87 | custom | hg38 | 9606 | Homo sapiens | genomic | 1 | 4 | 859 | 14 | 13 | 29 | 8 | ... |
88 +-----------+-----------+-------+--------------+-----------+-------------------+-------+----------+-----+-----+-----+-----+-----+
89
90 Example of CoCoPUTs style bicodon output, the majority of bicodons (codon pairs) have been removed in this example, for brevity:
91
92 +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
93 | Division | Assembly | Taxid | Species | Organelle | Translation Table | # CDS | # Codon Pairs | aaaaaa | aaaaac | aaaaag | aaaaat | ... |
94 +===========+===========+=======+==============+===========+===================+=======+===============+========+========+========+========+=====+
95 | custom | hg38 | 9606 | Homo sapiens | genomic | 1 | 4 | 859 | 0 | 0 | 0 | 1 | ... |
96 +-----------+-----------+-------+--------------+-----------+-------------------+-------+---------------+--------+--------+--------+--------+-----+
97 ]]></help>
98 <expand macro="citations"/>
99 </tool>