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comparison eggnog_mapper_annotate.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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12:9d1fbff733cf 13:844fa988236b
1 <tool id="eggnog_mapper_annotate" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>annotation phase</description>
3 <macros>
4 <import>eggnog_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 @MERGE_ANNOTATIONS@
10
11 emapper.py
12 @DB_TOKEN@
13 -m no_search
14 @ORTHO_SEARCH_TOKEN@
15
16 @ANNOTATION_TOKEN@
17 $output_options.no_file_comments
18 $output_options.report_orthologs
19 $output_options.md5
20 --output='results'
21 --cpu "\${GALAXY_SLOTS:-1}"
22 --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
23 --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
24 ]]></command>
25 <inputs>
26 <expand macro="db_macro"/>
27 <expand macro="ortho_annotate_macro"/>
28
29 <section name="annotation_options" title="Annotation options">
30 <expand macro="annotation_options_macro"/>
31 </section>
32
33 <expand macro="output_options_annotate_macro"/>
34 </inputs>
35 <outputs>
36 <expand macro="annotation_output_macro"/>
37 <expand macro="annotation_orthologs_output_macro"/>
38 </outputs>
39 <tests>
40 <!-- test producing annotations form seed orthologs -->
41 <test expect_num_outputs="1">
42 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
43 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
44 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
45 </param>
46 <conditional name="annotation_options">
47 </conditional>
48 <section name="output_options">
49 <param name="report_orthologs" value="false"/>
50 <param name="no_file_comments" value="true"/>
51 </section>
52 <expand macro="annotations_assertion"/>
53 <expand macro="stdout_assertion"/>
54 </test>
55
56 <!-- test using chached annotations from previous run -->
57 <test expect_num_outputs="2">
58 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
59 <conditional name="ortho_method">
60 <param name="m" value="cache"/>
61 <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
62 <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
63 </conditional>
64 <section name="output_options">
65 <param name="report_orthologs" value="true"/>
66 <param name="no_file_comments" value="true"/>
67 <param name="md5" value="true"/>
68 </section>
69 <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
70 <output name="no_annotations" ftype="fasta">
71 <assert_contents>
72 <has_n_lines n="0"/>
73 </assert_contents>
74 </output>
75 <expand macro="stdout_assertion"/>
76 </test>
77
78 <!-- test setting tax scope-->
79 <test expect_num_outputs="2">
80 <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
81 <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
82 <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
83 </param>
84 <section name="annotation_options">
85 <param name="tax_scope" value="651137" />
86 </section>
87 <section name="output_options">
88 <param name="report_orthologs" value="true"/>
89 <param name="no_file_comments" value="true"/>
90 </section>
91 <expand macro="annotations_assertion"/>
92 <expand macro="annotations_orthologs_assertion"/>
93 <expand macro="stdout_assertion">
94 <has_text text="--tax_scope=651137"/>
95 </expand>
96 </test>
97 </tests>
98 <help><![CDATA[
99
100 eggnog-mapper
101 =============
102 Overview
103 --------
104
105 ``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
106 Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
107 The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
108 as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
109
110 EggNOG-mapper is also available as a public online resource: `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
111
112 Outputs
113 -------
114
115 @HELP_ANNOTATION_OUTPUTS@
116
117 **Recommentation for large input data**
118
119 EggNOG-mapper consists of two phases
120
121 1. finding seed orthologous sequences (compute intensive)
122 2. expanding annotations (IO intensive)
123
124 by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
125 both phases are executed within one tool run.
126
127 For large input FASTA datasets in can be favourable to split this in two separate
128 tool runs as follows:
129
130 1. Split the FASTA (e.g. 1M seqs per data set)
131 2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
132 3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
133
134 See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
135
136 Another alternative is to use cached annotations (produced in a run with --md5 enabled).
137
138
139 ]]></help>
140 <expand macro="citations"/>
141 </tool>