--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eggnog_mapper_annotate.xml	Mon Sep 04 12:47:09 2023 +0000
@@ -0,0 +1,141 @@
+<tool id="eggnog_mapper_annotate" name="eggNOG Mapper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>annotation phase</description>
+    <macros>
+        <import>eggnog_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        @MERGE_ANNOTATIONS@
+
+        emapper.py
+        @DB_TOKEN@
+        -m no_search
+        @ORTHO_SEARCH_TOKEN@
+
+        @ANNOTATION_TOKEN@
+        $output_options.no_file_comments
+        $output_options.report_orthologs
+        $output_options.md5
+        --output='results'
+        --cpu "\${GALAXY_SLOTS:-1}"
+        --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
+        --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR}
+    ]]></command>
+    <inputs>
+        <expand macro="db_macro"/>
+        <expand macro="ortho_annotate_macro"/>
+
+        <section name="annotation_options" title="Annotation options">
+            <expand macro="annotation_options_macro"/>
+        </section>
+        
+        <expand macro="output_options_annotate_macro"/>
+    </inputs>
+    <outputs>
+        <expand macro="annotation_output_macro"/>
+        <expand macro="annotation_orthologs_output_macro"/>
+    </outputs>
+    <tests>
+        <!-- test producing annotations form seed orthologs -->
+        <test expect_num_outputs="1">
+            <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
+            <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
+                <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
+            </param>
+            <conditional name="annotation_options">
+            </conditional>
+            <section name="output_options">
+                <param name="report_orthologs" value="false"/>
+                <param name="no_file_comments" value="true"/>
+            </section>
+            <expand macro="annotations_assertion"/>
+            <expand macro="stdout_assertion"/>
+        </test>
+
+        <!-- test using chached annotations from previous run -->
+        <test expect_num_outputs="2">
+            <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
+            <conditional name="ortho_method">
+                <param name="m" value="cache"/>
+                <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
+                <param name="cache" value="DIA_nlim.emapper.annotations_cached" ftype="tabular"/>
+            </conditional>
+            <section name="output_options">
+                <param name="report_orthologs" value="true"/>
+                <param name="no_file_comments" value="true"/>
+                <param name="md5" value="true"/>
+            </section>
+            <expand macro="annotations_assertion" columns="22" add_metadata_columm_names=",md5" add_column_names="&#009;md5" add_column_re="\t[\d\w]+"/>
+            <output name="no_annotations" ftype="fasta">
+                <assert_contents>
+                    <has_n_lines n="0"/>
+                </assert_contents>
+            </output>
+            <expand macro="stdout_assertion"/>
+        </test>
+
+        <!-- test setting tax scope-->
+        <test expect_num_outputs="2">
+            <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
+            <param name="annotate_hits_table" value="DIA_nlim.emapper.seed_orthologs" ftype="tabular">
+                <!-- this has no effect at the moment since column_names can not be set in uploads <metadata name="column_names" value="@SEED_ORTHOLOG_COLUMNS@"/> -->
+            </param>
+            <section name="annotation_options">
+                <param name="tax_scope" value="651137" />
+            </section>
+            <section name="output_options">
+                <param name="report_orthologs" value="true"/>
+                <param name="no_file_comments" value="true"/>
+            </section>
+            <expand macro="annotations_assertion"/>
+            <expand macro="annotations_orthologs_assertion"/>
+            <expand macro="stdout_assertion">
+                <has_text text="--tax_scope=651137"/>
+            </expand>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+eggnog-mapper
+=============
+Overview
+--------
+
+``eggnog-mapper`` is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments.
+Obvious examples include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
+The use of orthology predictions for functional annotation is considered more precise than traditional homology searches,
+as it avoids transferring annotations from paralogs (duplicate genes with a higher chance of being involved in functional divergence).
+
+EggNOG-mapper is also available as a public online resource:  `<http://beta-eggnogdb.embl.de/#/app/emapper>`_.
+
+Outputs
+-------
+
+@HELP_ANNOTATION_OUTPUTS@
+
+**Recommentation for large input data**
+
+EggNOG-mapper consists of two phases
+
+1. finding seed orthologous sequences (compute intensive)
+2. expanding annotations (IO intensive)
+
+by default (i.e. if *Method to search seed orthologs* is not *Skip search stage...* and *Annotate seed orthologs* is *Yes*)
+both phases are executed within one tool run. 
+
+For large input FASTA datasets in can be favourable to split this in two separate
+tool runs as follows:
+
+1. Split the FASTA (e.g. 1M seqs per data set)
+2. Run the search phase only (set *Annotate seed orthologs* to *No*) on the separate FASTA files.
+3. Run the annotation phase (set *Method to search seed orthologs* to *Skip search stage...*)
+
+See [also](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs)
+
+Another alternative is to use cached annotations (produced in a run with --md5 enabled).
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>