Mercurial > repos > iuc > bicodon_counts_from_fasta
comparison bicodon_counts_from_fasta.xml @ 0:e13169dca7c8 draft default tip
"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 20:36:48 +0000 |
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-1:000000000000 | 0:e13169dca7c8 |
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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> |