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comparison drep_compare.xml @ 2:7de8436f7f97 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
author iuc
date Sat, 12 Feb 2022 17:38:03 +0000
parents a5054beafded
children dfe6041879b9
comparison
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1:a5054beafded 2:7de8436f7f97
1 <tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5"> 1 <tool id="drep_compare" name="dRep compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
2 <description>compare a list of genomes</description> 2 <description>compare a list of genomes</description>
3 <expand macro="bio_tools" /> 3 <expand macro="biotools" />
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @PREPARE_GENOMES@ 9 @PREPARE_GENOMES@
10 dRep compare outdir 10 dRep compare outdir
11 @GENOME_COMPARISON_OPTIONS@ 11 @GENOMES@
12 @CLUSTERING_OPTIONS@ 12 @COMPARISON_CLUSTERING_OPTIONS@
13 @TAXONOMY_OPTIONS@ 13 @WARNING_OPTIONS@
14 @WARNING_OPTIONS@
15 @GENOMES@
16 ]]></command> 14 ]]></command>
17 <inputs> 15 <inputs>
18 <expand macro="genomes"/> 16 <expand macro="genomes"/>
19 <expand macro="genome_comparison_options"/> 17 <expand macro="comparison_clustering_options"/>
20 <expand macro="clustering_options"/>
21 <expand macro="taxonomy_options"/>
22 <expand macro="warning_options"/> 18 <expand macro="warning_options"/>
23 <expand macro="select_outputs"/> 19 <expand macro="select_outputs"/>
24 </inputs> 20 </inputs>
25 <outputs> 21 <outputs>
26 <expand macro="common_outputs" /> 22 <expand macro="common_outputs" />
27 </outputs> 23 </outputs>
28 <tests> 24 <tests>
29 <expand macro="test_defaults_log"> 25 <test expect_num_outputs="4">
30 <has_text text="dRep compare finished" /> 26 <expand macro="test_string_inputs"/>
31 </expand> 27 <expand macro="test_default_comparison_clustering_options"/>
28 <expand macro="test_default_warning_options"/>
29 <expand macro="test_default_select_outputs"/>
30 <expand macro="test_log_output">
31 <has_text text="dRep compare finished" />
32 </expand>
33 </test>
34 <test expect_num_outputs="4">
35 <expand macro="test_integer_inputs"/>
36 <expand macro="test_default_comparison_clustering_options"/>
37 <expand macro="test_default_warning_options"/>
38 <expand macro="test_default_select_outputs"/>
39 <expand macro="test_log_output">
40 <has_text text="dRep compare finished" />
41 </expand>
42 </test>
32 </tests> 43 </tests>
33 <help><![CDATA[ 44 <help><![CDATA[
34 **dRep compare** 45 **dRep compare**
35 46
36 `dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets. 47 `dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets.
38 `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). 49 `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).
39 50
40 dRep performs this in two steps: 51 dRep performs this in two steps:
41 52
42 - first with a rapid primary algorithm (Mash) 53 - first with a rapid primary algorithm (Mash)
43 - second with a more sensitive algorithm (ANIm). 54 - second with a more sensitive algorithm (ANIm).
44 55
45 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. 56 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.
46 57
47 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. 58 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.
48 59
49 60
50 **INPUTS** 61 **INPUTS**