Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper_search.xml @ 12:a5d5e84eed93 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
author galaxyp
date Mon, 19 Jan 2026 22:22:38 +0000
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12
a5d5e84eed93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 0e3cff872b53efe21cbf4905ed0b072337192001
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1 <tool id="eggnog_mapper_search" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>search phase</description>
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3 <macros>
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4 <import>eggnog_macros.xml</import>
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5 </macros>
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 emapper.py
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11 --no_annot ## only search, i.e. no annotation
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12 @DB_TOKEN@
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13 @ORTHO_SEARCH_TOKEN@
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14
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15 $output_options.no_file_comments
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16 --output='results'
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17 --cpu "\${GALAXY_SLOTS:-4}"
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18 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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19 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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20 ]]></command>
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21 <inputs>
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22 <expand macro="db_macro"/>
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23 <expand macro="ortho_search_macro"/>
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24 <expand macro="output_options_macro"/>
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25 </inputs>
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26 <outputs>
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27 <expand macro="ortho_search_output_macro"/>
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28 </outputs>
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29 <tests>
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30 <!-- test producing only seed orthologs-->
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31 <test expect_num_outputs="1">
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32 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
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33 <conditional name="ortho_method">
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34 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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35 </conditional>
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36 <section name="output_options">
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37 <param name="no_file_comments" value="true"/>
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38 </section>
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39 <expand macro="seed_orthologs_assertion"/>
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40 <expand macro="stdout_assertion"/>
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41 </test>
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42
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43 <!-- test setting a diamond option-->
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44 <test expect_num_outputs="1">
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45 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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46 <conditional name="ortho_method">
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47 <param name="m" value="diamond" />
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48 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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49 <param name="sensmode" value="fast" />
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50 </conditional>
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51 <section name="output_options">
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52 <param name="no_file_comments" value="true"/>
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53 </section>
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54 <expand macro="seed_orthologs_assertion"/>
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55 <expand macro="stdout_assertion">
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56 <has_text text="--sensmode fast"/>
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57 </expand>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61
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62 eggnog-mapper
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63 =============
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64 Overview
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65 --------
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66
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67 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
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68 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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69 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
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70 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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71
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72 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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73
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74 Outputs
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75 -------
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76
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77 @HELP_SEARCH_OUTPUTS@
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78
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79 **Recommentation for large input data**
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80
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81 EggNOG-mapper consists of two phases
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82
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83 1. finding seed orthologous sequences (compute intensive)
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84 2. expanding annotations (IO intensive)
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85
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86 by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
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87 both phases are executed within one tool run.
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88
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89 For large input FASTA datasets in can be favourable to split this in two separate
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90 tool runs as follows:
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91
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92 1. Split the FASTA (e.g. 1M seqs per data set)
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93 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
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94 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
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95
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96 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
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97
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98 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
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99
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100
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101 ]]></help>
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102 <expand macro="citations"/>
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103 </tool>