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comparison 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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11:1f2be4ae431f 12:a5d5e84eed93
1 <tool id="eggnog_mapper_search" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>search phase</description>
3 <macros>
4 <import>eggnog_macros.xml</import>
5 </macros>
6 <expand macro="biotools"/>
7 <expand macro="requirements"/>
8 <expand macro="version_command"/>
9 <command detect_errors="aggressive"><![CDATA[
10 emapper.py
11 --no_annot ## only search, i.e. no annotation
12 @DB_TOKEN@
13 @ORTHO_SEARCH_TOKEN@
14
15 $output_options.no_file_comments
16 --output='results'
17 --cpu "\${GALAXY_SLOTS:-4}"
18 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
19 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
20 ]]></command>
21 <inputs>
22 <expand macro="db_macro"/>
23 <expand macro="ortho_search_macro"/>
24 <expand macro="output_options_macro"/>
25 </inputs>
26 <outputs>
27 <expand macro="ortho_search_output_macro"/>
28 </outputs>
29 <tests>
30 <!-- test producing only seed orthologs-->
31 <test expect_num_outputs="1">
32 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
33 <conditional name="ortho_method">
34 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
35 </conditional>
36 <section name="output_options">
37 <param name="no_file_comments" value="true"/>
38 </section>
39 <expand macro="seed_orthologs_assertion"/>
40 <expand macro="stdout_assertion"/>
41 </test>
42
43 <!-- test setting a diamond option-->
44 <test expect_num_outputs="1">
45 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
46 <conditional name="ortho_method">
47 <param name="m" value="diamond" />
48 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
49 <param name="sensmode" value="fast" />
50 </conditional>
51 <section name="output_options">
52 <param name="no_file_comments" value="true"/>
53 </section>
54 <expand macro="seed_orthologs_assertion"/>
55 <expand macro="stdout_assertion">
56 <has_text text="--sensmode fast"/>
57 </expand>
58 </test>
59 </tests>
60 <help><![CDATA[
61
62 eggnog-mapper
63 =============
64 Overview
65 --------
66
67 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
68 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
69 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
70 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
71
72 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
73
74 Outputs
75 -------
76
77 @HELP_SEARCH_OUTPUTS@
78
79 **Recommentation for large input data**
80
81 EggNOG-mapper consists of two phases
82
83 1. finding seed orthologous sequences (compute intensive)
84 2. expanding annotations (IO intensive)
85
86 by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
87 both phases are executed within one tool run.
88
89 For large input FASTA datasets in can be favourable to split this in two separate
90 tool runs as follows:
91
92 1. Split the FASTA (e.g. 1M seqs per data set)
93 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
94 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
95
96 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
97
98 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
99
100
101 ]]></help>
102 <expand macro="citations"/>
103 </tool>