Mercurial > repos > galaxyp > eggnog_mapper

annotate eggnog_mapper_search.xml @ 13:844fa988236b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
author galaxyp
date Mon, 04 Sep 2023 12:47:09 +0000
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13
844fa988236b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 468bd31b8858adbba2854f118e4cbe31f4cd68cb
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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="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 emapper.py
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10 @DB_TOKEN@
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11 @ORTHO_SEARCH_TOKEN@
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12
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13 $output_options.no_file_comments
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14 --output='results'
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15 --cpu "\${GALAXY_SLOTS:-4}"
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16 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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17 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
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18 ]]></command>
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19 <inputs>
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20 <expand macro="db_macro"/>
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21 <expand macro="ortho_search_macro"/>
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22 <expand macro="output_options_macro"/>
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23 </inputs>
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24 <outputs>
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25 <expand macro="ortho_search_output_macro"/>
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26 </outputs>
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27 <tests>
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28 <!-- test producing only seed orthologs-->
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29 <test expect_num_outputs="1">
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30 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
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31 <conditional name="ortho_method">
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32 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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33 </conditional>
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34 <section name="output_options">
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35 <param name="no_file_comments" value="true"/>
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36 </section>
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37 <expand macro="seed_orthologs_assertion"/>
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38 <expand macro="stdout_assertion"/>
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39 </test>
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40
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41 <!-- test setting a diamond option-->
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42 <test expect_num_outputs="1">
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43 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
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44 <conditional name="ortho_method">
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45 <param name="m" value="diamond" />
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46 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
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47 <param name="sensmode" value="fast" />
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48 </conditional>
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49 <section name="output_options">
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50 <param name="no_file_comments" value="true"/>
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51 </section>
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52 <expand macro="seed_orthologs_assertion"/>
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53 <expand macro="stdout_assertion">
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54 <has_text text="--sensmode fast"/>
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55 </expand>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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60 eggnog-mapper
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61 =============
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62 Overview
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63 --------
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64
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65 ``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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66 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
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67 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
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68 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
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69
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70 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
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72 Outputs
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73 -------
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75 @HELP_SEARCH_OUTPUTS@
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77 **Recommentation for large input data**
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79 EggNOG-mapper consists of two phases
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80
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81 1. finding seed orthologous sequences (compute intensive)
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82 2. expanding annotations (IO intensive)
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83
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84 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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85 both phases are executed within one tool run.
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86
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87 For large input FASTA datasets in can be favourable to split this in two separate
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88 tool runs as follows:
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89
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90 1. Split the FASTA (e.g. 1M seqs per data set)
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91 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
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92 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
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93
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94 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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95
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96 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
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97
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98
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99 ]]></help>
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100 <expand macro="citations"/>
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101 </tool>