Mercurial > repos > iuc > drep_dereplicate

annotate drep_dereplicate.xml @ 8:caaf7cbaafbf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 00dc2cd8c229b7a0f05c0ca2520098c132f40793
author iuc
date Mon, 14 Apr 2025 18:11:33 +0000
parents c55eec39f086
children
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6
055649d1378e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit bf3d3fb4a7c0ad2c6942955783bf15cda7754b28
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1 <tool id="drep_dereplicate" name="dRep dereplicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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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>
6
055649d1378e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit bf3d3fb4a7c0ad2c6942955783bf15cda7754b28
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6 <expand macro="biotools" />
2
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7 <expand macro="requirements">
8
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8 <requirement type="package" version="1.2.3">checkm-genome</requirement>
2
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9 </expand>
0
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10 <command detect_errors="exit_code"><![CDATA[
7
c55eec39f086 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 620124793ed18545728d07cfd8592065bc5c6c2d
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11 @PREPARE_GENOMES@
c55eec39f086 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 620124793ed18545728d07cfd8592065bc5c6c2d
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12 dRep
c55eec39f086 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 620124793ed18545728d07cfd8592065bc5c6c2d
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13 dereplicate
c55eec39f086 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 620124793ed18545728d07cfd8592065bc5c6c2d
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14 outdir
c55eec39f086 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 620124793ed18545728d07cfd8592065bc5c6c2d
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15 @GENOMES@
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16 @FILTER_OPTIONS@
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17 @QUALITY_ASSESSMENT_OPTIONS@
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18 @COMPARISON_CLUSTERING_OPTIONS@
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19 @SCORING_OPTIONS@
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20 @WARNING_OPTIONS@
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21 --processors \${GALAXY_SLOTS:-1}
2
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22 || (rc=\$?;
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23 ls -ltr `find outdir -type f`;
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24 cat outdir/data/checkM/checkM_outdir/checkm.log;
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25 cat outdir/log/logger.log;
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26 exit \$rc)
0
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27 ]]></command>
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28 <inputs>
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29 <expand macro="genomes"/>
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30 <expand macro="filtering_options"/>
2
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31 <expand macro="quality_assessment_options"/>
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32 <expand macro="comparison_clustering_options"/>
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33 <expand macro="scoring_options"/>
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34 <expand macro="warning_options"/>
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35 <expand macro="select_drep_outputs"/>
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36 </inputs>
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37 <outputs>
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38 <collection name="dereplicated_genomes" type="list" label="dereplicated_genomes">
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39 <discover_datasets pattern="__designation__" directory="outdir/dereplicated_genomes" ext='fasta'/>
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40 </collection>
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41 <expand macro="drep_outputs" />
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42 </outputs>
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43 <tests>
2
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44 <test expect_num_outputs="8">
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45 <expand macro="test_string_inputs"/>
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46 <expand macro="test_default_filtering_options"/>
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47 <expand macro="test_default_quality_assessment_options"/>
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48 <expand macro="test_default_comparison_clustering_options"/>
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49 <expand macro="test_default_scoring_options"/>
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50 <expand macro="test_default_warning_options"/>
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51 <expand macro="test_default_select_drep_outputs"/>
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52 <expand macro="test_log_output">
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53 <has_text text="dRep dereplicate finished" />
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54 </expand>
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55 </test>
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56 <test expect_num_outputs="8">
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57 <expand macro="test_integer_inputs"/>
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58 <expand macro="test_default_filtering_options"/>
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59 <expand macro="test_default_quality_assessment_options"/>
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60 <expand macro="test_default_comparison_clustering_options"/>
4
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61 <expand macro="test_extra_weight_table_scoring_options"/>
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62 <expand macro="test_default_warning_options"/>
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63 <expand macro="test_default_select_drep_outputs"/>
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64 <expand macro="test_log_output">
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65 <has_text text="dRep dereplicate finished" />
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66 </expand>
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67 </test>
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68 <test expect_num_outputs="8">
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69 <expand macro="test_string_inputs"/>
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70 <expand macro="test_default_filtering_options"/>
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71 <expand macro="test_default_quality_assessment_options"/>
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72 <expand macro="test_default_comparison_clustering_options"/>
2
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73 <expand macro="test_default_scoring_options"/>
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74 <expand macro="test_default_warning_options"/>
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75 <expand macro="test_default_select_drep_outputs"/>
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76 <expand macro="test_log_output">
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77 <has_text text="dRep dereplicate finished" />
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78 </expand>
0
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 **dRep dereplicate**
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83
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84 `dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets.
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85
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86 `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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87
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88 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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89
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90 The steps to this process are:
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91
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92 - Assemble each sample separately using your favorite assembler. You can also perform a co-assembly to catch low-abundance microbes
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93 - Bin each assembly (and co-assembly) separately using your favorite binner
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94 - Pull the bins from all assemblies together and run **dRep** on them
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95 - Perform downstream analysis on the de-replicated genome list
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96
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97
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98
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99 **INPUTS**
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100
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101 - Genome sets in fasta format.
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102
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103
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104 **OUTPUTS**
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105
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106 - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs.
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107 - `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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108 - A Dataset collection of the “best” genome of each secondary cluster.
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109 - `Tables from intermediate steps <https://drep.readthedocs.io/en/latest/advanced_use.html>`_
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110
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111 * Chdb.csv # CheckM results for Bdb
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112 * Widb.csv # Winning genomes' checkM information
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113
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114
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115 ]]></help>
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116 <expand macro="citations" />
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117 </tool>