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annotate drep_compare.xml @ 3:d99788b71ce7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad
author iuc
date Wed, 15 Mar 2023 11:04:40 +0000
parents 7157accd23d0
children 9902c85117a4
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1 <tool id="drep_compare" name="dRep compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="3.5">
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2 <description>compare a list of genomes</description>
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3 <expand macro="biotools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @PREPARE_GENOMES@
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10 dRep compare outdir
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11 @GENOMES@
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12 @COMPARISON_CLUSTERING_OPTIONS@
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13 @WARNING_OPTIONS@
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14 ]]></command>
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15 <inputs>
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16 <expand macro="genomes"/>
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17 <expand macro="comparison_clustering_options"/>
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18 <expand macro="warning_options"/>
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19 <expand macro="select_outputs"/>
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20 </inputs>
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21 <outputs>
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22 <expand macro="common_outputs" />
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23 </outputs>
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24 <tests>
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25 <test expect_num_outputs="4">
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26 <expand macro="test_string_inputs"/>
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27 <expand macro="test_default_comparison_clustering_options"/>
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28 <expand macro="test_default_warning_options"/>
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29 <expand macro="test_default_select_outputs"/>
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30 <expand macro="test_log_output">
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31 <has_text text="dRep compare finished" />
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32 </expand>
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33 </test>
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34 <test expect_num_outputs="4">
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35 <expand macro="test_integer_inputs"/>
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36 <expand macro="test_default_comparison_clustering_options"/>
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37 <expand macro="test_default_warning_options"/>
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38 <expand macro="test_default_select_outputs"/>
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39 <expand macro="test_log_output">
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40 <has_text text="dRep compare finished" />
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41 </expand>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 **dRep compare**
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47 `dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets.
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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).
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51 dRep performs this in two steps:
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53 - first with a rapid primary algorithm (Mash)
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54 - second with a more sensitive algorithm (ANIm).
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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.
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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.
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61 **INPUTS**
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63 - Genome sets in fasta format.
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66 **OUTPUTS**
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68 - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs.
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69 - `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.
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72 ]]></help>
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73 <expand macro="citations" />
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74 </tool>