Mercurial > repos > iuc > drep_dereplicate

annotate drep_dereplicate.xml @ 0:8dfcdbeaeed8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
author iuc
date Tue, 05 May 2020 06:12:47 -0400
parents
children ef7cd2e7bc05
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8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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1 <tool id="drep_dereplicate" name="dRep dereplicate" version="@VERSION@.0" python_template_version="3.5">
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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2 <description>De-replicate a list of genomes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @PREPARE_GENOMES@
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9 dRep dereplicate outdir
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10 @FILTER_OPTIONS@
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11 @GENOME_COMPARISON_OPTIONS@
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12 @CLUSTERING_OPTIONS@
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13 @SCORING_OPTIONS@
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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14 @TAXONOMY_OPTIONS@
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15 @WARNING_OPTIONS@
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16 @GENOMES@
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17 --debug
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18 || (rc=\$?;
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19 ls -ltr `find outdir -type f`;
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20 cat outdir/data/checkM/checkM_outdir/checkm.log;
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21 cat outdir/log/logger.log;
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22 exit \$rc)
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23 ]]></command>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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24 <inputs>
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25 <expand macro="genomes"/>
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26 <expand macro="filtering_options"/>
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27 <expand macro="genome_comparison_options"/>
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28 <expand macro="clustering_options"/>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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29 <expand macro="scoring_options"/>
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30 <expand macro="taxonomy_options"/>
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31 <expand macro="warning_options"/>
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32 <expand macro="select_drep_outputs"/>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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33 </inputs>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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34 <outputs>
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35 <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes">
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36 <discover_datasets pattern="__designation__" directory="outdir/dereplicated_genomes" ext='fasta'/>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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37 </collection>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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38 <expand macro="drep_outputs" />
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39 </outputs>
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40 <tests>
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41 <expand macro="test_defaults_log">
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42 <has_text text="dRep dereplicate finished" />
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43 </expand>
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44 <test>
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45 <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>
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46 <conditional name="filter">
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47 <param name="set_options" value="yes"/>
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48 <conditional name="quality">
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49 <param name="source" value="checkm"/>
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50 <param name="checkM_method" value="taxonomy_wf"/>
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51 </conditional>
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52 </conditional>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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53 <output name="log">
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54 <assert_contents>
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55 <has_text text="dRep dereplicate finished" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 **dRep dereplicate**
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62
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63 `dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets.
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64
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65
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66
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67
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68
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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69 `De-replication <https://drep.readthedocs.io/en/latest/overview.html#genome-de-replication>`_ is the process of identifying sets of genomes that are the “same” in a list of genomes, and removing all but the “best” genome from each redundant set. How similar genomes need to be to be considered “same”, how to determine which genome is “best”, and other important decisions are discussed in `Choosing parameters. <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ Detailed options for each module are described at: https://drep.readthedocs.io/en/latest/module_descriptions.html
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70
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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71 A common use for genome de-replication is the case of individual assembly of metagenomic data. If metagenomic samples are collected in a series, a common way to assemble the short reads is with a “co-assembly”. That is, combining the reads from all samples and assembling them together. The problem with this is assembling similar strains together can severely fragment assemblies, precluding recovery of a good genome bin. An alternative option is to assemble each sample separately, and then “de-replicate” the bins from each assembly to make a final genome set.
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72
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73 The steps to this process are:
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74
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75 - Assemble each sample separately using your favorite assembler. You can also perform a co-assembly to catch low-abundance microbes
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76 - Bin each assembly (and co-assembly) separately using your favorite binner
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77 - Pull the bins from all assemblies together and run **dRep** on them
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78 - Perform downstream analysis on the de-replicated genome list
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79
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80
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81
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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82 **INPUTS**
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83
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84 - Genome sets in fasta format.
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85
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86
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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87 **OUTPUTS**
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88
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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89 - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs.
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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90 - `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.
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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91 - A Dataset collection of the “best” genome of each secondary cluster.
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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92 - `Tables from intermediate steps <https://drep.readthedocs.io/en/latest/advanced_use.html>`_
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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93
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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94 * Chdb.csv # CheckM results for Bdb
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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95 * Widb.csv # Winning genomes' checkM information
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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96
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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97
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98 ]]></help>
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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99 <expand macro="citations" />
8dfcdbeaeed8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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100 </tool>