Mercurial > repos > iuc > drep_compare
comparison drep_compare.xml @ 0:ef1c257adcbd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
author | iuc |
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date | Tue, 05 May 2020 06:20:45 -0400 |
parents | |
children | 7157accd23d0 |
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1 <tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5"> | |
2 <description>compare a list of genomes</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 @PREPARE_GENOMES@ | |
9 dRep compare outdir | |
10 @GENOME_COMPARISON_OPTIONS@ | |
11 @CLUSTERING_OPTIONS@ | |
12 @TAXONOMY_OPTIONS@ | |
13 @WARNING_OPTIONS@ | |
14 @GENOMES@ | |
15 ]]></command> | |
16 <inputs> | |
17 <expand macro="genomes"/> | |
18 <expand macro="genome_comparison_options"/> | |
19 <expand macro="clustering_options"/> | |
20 <expand macro="taxonomy_options"/> | |
21 <expand macro="warning_options"/> | |
22 <expand macro="select_outputs"/> | |
23 </inputs> | |
24 <outputs> | |
25 <expand macro="common_outputs" /> | |
26 </outputs> | |
27 <tests> | |
28 <expand macro="test_defaults_log"> | |
29 <has_text text="dRep compare finished" /> | |
30 </expand> | |
31 </tests> | |
32 <help><![CDATA[ | |
33 **dRep compare** | |
34 | |
35 `dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets. | |
36 | |
37 `dRep compare <https://drep.readthedocs.io/en/latest/overview.html#genome-comparison>`_ can rapidly and accurately compare a list of genomes in a pair-wise manner. This allows identification of groups of organisms that share similar DNA content in terms of Average Nucleotide Identity (ANI). | |
38 | |
39 dRep performs this in two steps: | |
40 | |
41 - first with a rapid primary algorithm (Mash) | |
42 - second with a more sensitive algorithm (ANIm). | |
43 | |
44 We can’t just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ and `Module Descriptions <https://drep.readthedocs.io/en/latest/module_descriptions.html>`_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists. | |
45 | |
46 dRep first compares all genomes using Mash, and then only runs the secondary algorithm (ANIm or gANI) on sets of genomes that have at least 90% Mash ANI. This results in a great decrease in the number of (slow) secondary comparisons that need to be run while maintaining the sensitivity of ANIm. | |
47 | |
48 | |
49 **INPUTS** | |
50 | |
51 - Genome sets in fasta format. | |
52 | |
53 | |
54 **OUTPUTS** | |
55 | |
56 - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs. | |
57 - `Warnings <https://drep.readthedocs.io/en/latest/example_output.html#warnings>`_ report two things: de-replicated genome similarity and secondary clusters that were almost different. | |
58 | |
59 | |
60 ]]></help> | |
61 <expand macro="citations" /> | |
62 </tool> |