Mercurial > repos > iuc > drep_compare
comparison drep_compare.xml @ 1:7157accd23d0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
author | iuc |
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date | Sat, 12 Feb 2022 17:40:04 +0000 |
parents | ef1c257adcbd |
children | 9902c85117a4 |
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0:ef1c257adcbd | 1:7157accd23d0 |
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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="biotools" /> | |
3 <macros> | 4 <macros> |
4 <import>macros.xml</import> | 5 <import>macros.xml</import> |
5 </macros> | 6 </macros> |
6 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
8 @PREPARE_GENOMES@ | 9 @PREPARE_GENOMES@ |
9 dRep compare outdir | 10 dRep compare outdir |
10 @GENOME_COMPARISON_OPTIONS@ | 11 @GENOMES@ |
11 @CLUSTERING_OPTIONS@ | 12 @COMPARISON_CLUSTERING_OPTIONS@ |
12 @TAXONOMY_OPTIONS@ | 13 @WARNING_OPTIONS@ |
13 @WARNING_OPTIONS@ | |
14 @GENOMES@ | |
15 ]]></command> | 14 ]]></command> |
16 <inputs> | 15 <inputs> |
17 <expand macro="genomes"/> | 16 <expand macro="genomes"/> |
18 <expand macro="genome_comparison_options"/> | 17 <expand macro="comparison_clustering_options"/> |
19 <expand macro="clustering_options"/> | |
20 <expand macro="taxonomy_options"/> | |
21 <expand macro="warning_options"/> | 18 <expand macro="warning_options"/> |
22 <expand macro="select_outputs"/> | 19 <expand macro="select_outputs"/> |
23 </inputs> | 20 </inputs> |
24 <outputs> | 21 <outputs> |
25 <expand macro="common_outputs" /> | 22 <expand macro="common_outputs" /> |
26 </outputs> | 23 </outputs> |
27 <tests> | 24 <tests> |
28 <expand macro="test_defaults_log"> | 25 <test expect_num_outputs="4"> |
29 <has_text text="dRep compare finished" /> | 26 <expand macro="test_string_inputs"/> |
30 </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> | |
31 </tests> | 43 </tests> |
32 <help><![CDATA[ | 44 <help><![CDATA[ |
33 **dRep compare** | 45 **dRep compare** |
34 | 46 |
35 `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. |
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). | 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). |
38 | 50 |
39 dRep performs this in two steps: | 51 dRep performs this in two steps: |
40 | 52 |
41 - first with a rapid primary algorithm (Mash) | 53 - first with a rapid primary algorithm (Mash) |
42 - second with a more sensitive algorithm (ANIm). | 54 - second with a more sensitive algorithm (ANIm). |
43 | 55 |
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. | 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. |
45 | 57 |
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. | 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. |
47 | 59 |
48 | 60 |
49 **INPUTS** | 61 **INPUTS** |