--- a/eggnog_macros.xml	Mon Jun 20 12:49:52 2022 +0000
+++ b/eggnog_macros.xml	Tue Jul 19 15:14:52 2022 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
    <token name="@TOOL_VERSION@">2.1.8</token>
-   <token name="@VERSION_SUFFIX@">2.1.8</token>
+   <token name="@VERSION_SUFFIX@">3</token>
    <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
     <!--
     # DB versionning was super confusing for eggnog-mapper 2.0.x:
@@ -64,10 +64,82 @@
             </output>
         </test>
     </xml>
+
+    <xml name="fasta_input">
+        <param argument="-i" name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
+        <conditional name="input_trans">
+            <param argument="--itype" type="select" label="Type of sequences">
+                <option value="proteins" selected="true">proteins</option>
+                <option value="CDS">CDS</option>
+                <option value="genome">genome</option>
+                <option value="metagenome">metagenome</option>
+            </param>
+            <when value="proteins"/>
+            <when value="CDS">
+                <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
+                    label="Translate CDS to proteins before search"/>
+            </when>
+            <when value="genome">
+                <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
+                    label="Translate predicted CDS from blastx hits to proteins"/>
+                <param argument="--genepred" type="select" label="Type of sequences">
+                    <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
+                    <option value="prodigal" selected="true">Performed using Prodigal</option>
+                </param>
+            </when>
+            <when value="metagenome">
+                <param argument="--translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
+                    label="Translate predicted CDS from blastx hits to proteins"/>
+                <param argument="--genepred" type="select" label="Type of sequences">
+                    <option value="search">Inferred from Diamond/MMseqs2 blastx hits</option>
+                    <option value="prodigal" selected="true">Performed using Prodigal</option>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <!-- Common options for search filtering (applies to diamond and mmseqs only) -->
+    <xml name="common_search_options">
+        <param argument="--query_cover" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" />
+        <param argument="--subject_cover" type="integer" optional="true" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" />
+        <param argument="--pident" type="integer" optional="true" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of identity" />
+        <param argument="--evalue" type="float" optional="true" min="0" label="Minimum query coverage" help="Report only alignments below or equal the e-value" />
+        <param argument="--score" type="float" value="0.001" optional="true" min="0" label="Minimum query coverage" help="Report only alignments above or equal the score" />
+    </xml>
+    <token name="@SEED_ORTHOLOG_COLUMNS@">query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov</token>
+    
     <xml name="stdout_assertion">
         <assert_stdout>
             <has_line line="#  emapper-@TOOL_VERSION@"/>
             <has_line line="FINISHED"/>
+            <yield/>
         </assert_stdout>
     </xml>
+    <xml name="seed_orthologs_assertion">
+        <output name="seed_orthologs" ftype="tabular">
+            <assert_contents>
+                <has_line line="#qseqid&#009;sseqid&#009;evalue&#009;bitscore&#009;qstart&#009;qend&#009;sstart&#009;send&#009;pident&#009;qcov&#009;scov"/>
+                <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\d+){4}(\t[.\d]+){3}" n="1"/>
+            </assert_contents>
+        </output>
+    </xml>
+    <xml name="annotations_assertion" token_columns="21" token_add_metadata_columm_names="" token_add_column_names="" token_add_column_re="">
+        <output name="annotations" ftype="tabular">
+            <metadata name="columns" value="@COLUMNS@" />
+            <!-- <metadata name="column_names" value="query,seed_ortholog,evalue,score,max_annot_lvl,COG_category,Description,Preferred_name,GOs,EC,KEGG_ko,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reaction,PFAMseggNOG_OGs@ADD_METADATA_COLUMN_NAMES@" /> -->
+            <assert_contents>
+                <has_line line="#query&#009;seed_ortholog&#009;evalue&#009;score&#009;eggNOG_OGs&#009;max_annot_lvl&#009;COG_category&#009;Description&#009;Preferred_name&#009;GOs&#009;EC&#009;KEGG_ko&#009;KEGG_Pathway&#009;KEGG_Module&#009;KEGG_Reaction&#009;KEGG_rclass&#009;BRITE&#009;KEGG_TC&#009;CAZy&#009;BiGG_Reaction&#009;PFAMs@ADD_COLUMN_NAMES@"/>
+                <has_line_matching expression="(\S+\t){2}[-+.e\d]+\t[.\d]+(\t\S+){7}\tko:\S+(\t\S+){9}@ADD_COLUMN_RE@" n="1"/>
+            </assert_contents>
+        </output>
+    </xml>
+    <xml name="annotations_orthologs_assertion">
+        <output name="annotations_orthologs" ftype="tabular">
+            <metadata name="columns" value="4" />
+            <metadata name="column_names" value="query,orth_type,species,orthologs" />
+            <assert_contents>
+                <has_line line="#query&#009;orth_type&#009;species&#009;orthologs"/>
+                <has_line_matching expression="\S+\t(one2one|many2one|one2many|many2many|seed)(\t[^\t]+){2}" n="2"/>
+            </assert_contents>
+        </output>
+    </xml>
 </macros>