diff eggnog_mapper.xml @ 6:3cb37af59360 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author galaxyp
date Sat, 05 Sep 2020 07:21:28 +0000
parents a5a3bdd0954b
children 4e4c6329f6cd
line wrap: on
line diff
--- a/eggnog_mapper.xml	Mon Nov 11 11:50:36 2019 -0500
+++ b/eggnog_mapper.xml	Sat Sep 05 07:21:28 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@.1">
+<tool id="eggnog_mapper" name="eggNOG Mapper" version="@VERSION@">
     <description>functional sequence annotation by orthology</description>
     <macros>
         <import>eggnog_macros.xml</import>
@@ -8,28 +8,15 @@
     <command detect_errors="aggressive"><![CDATA[
         emapper.py
         --data_dir '$eggnog_data.fields.path'
-        -m $db.mode 
+        -m diamond
         $translate
-        #if ($db.mode == 'hmmer'):
-            #if $db.database.fields.path:
-                --database=$db.database.fields.path
-            #else
-                --database=$db.database
-            #end if
-            #if $db.hmm_options.hmm_settings == 'specified':
-                --hmm_maxhits=$db.hmm_options.hmm_maxhits
-                --hmm_evalue=$db.hmm_options.hmm_evalue
-                --hmm_score=$db.hmm_options.hmm_score
-                --hmm_maxseqlen=$db.hmm_options.hmm_maxseqlen
-                #if str($db.hmm_options.hmm_qcov):
-                    --hmm_qcov=$db.hmm_options.hmm_qcov
-                #end if
-                --Z=$db.hmm_options.Z
-            #end if
-        #elif ($db.mode == 'diamond'):
-            --matrix '$db.matrix_gapcosts.matrix'
-            $db.matrix_gapcosts.gap_costs
-        #end if
+
+        ## Diamond option
+        --matrix '$diamond.matrix_gapcosts.matrix'
+        $diamond.matrix_gapcosts.gap_costs
+        --query-cover $diamond.query_cover
+        --subject-cover $diamond.subject_cover
+
         #if $annotation_options.tax_scope:
             --tax_scope=$annotation_options.tax_scope
         #end if
@@ -40,10 +27,10 @@
             --go_evidence=$annotation_options.go_evidence
         #end if
         #if $seed_ortholog_options.seed_ortholog_evalue:
-            --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue 
+            --seed_ortholog_evalue=$seed_ortholog_options.seed_ortholog_evalue
         #end if
         #if str($seed_ortholog_options.seed_ortholog_score):
-            --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score 
+            --seed_ortholog_score=$seed_ortholog_options.seed_ortholog_score
         #end if
         $output_options.no_file_comments
         $output_options.no_annot
@@ -52,286 +39,149 @@
         -i '${input}'
         --cpu "\${GALAXY_SLOTS:-4}"
     ]]></command>
-        <inputs>
-            <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
-            <param name="eggnog_data" type="select" label="Version of eggNOG Database">
-                <options from_data_table="eggnog_mapper_db"/>
-            </param>
-            <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
-                label="Are these coding DNA sequences that need to be translated?"/>
-            <conditional name="db">
-                <param name="mode" type="select" label="Annotation Type">
-                    <option value="hmmer">HMM</option>
-                    <option value="diamond">DIAMOND</option>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Fasta sequences to annotate"/>
+        <param name="eggnog_data" type="select" label="Version of eggNOG Database">
+            <options from_data_table="eggnog_mapper_db"/>
+        </param>
+        <param name="translate" type="boolean" truevalue="--translate" falsevalue="" checked="false"
+            label="Are these coding DNA sequences that need to be translated?"/>
+
+        <section name="diamond" expanded="true" title="Diamond Options">
+            <conditional name="matrix_gapcosts">
+                <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
+                    <option value="BLOSUM90">BLOSUM90</option>
+                    <option value="BLOSUM80">BLOSUM80</option>
+                    <option value="BLOSUM62" selected="true">BLOSUM62</option>
+                    <option value="BLOSUM50">BLOSUM50</option>
+                    <option value="BLOSUM45">BLOSUM45</option>
+                    <option value="PAM250">PAM250</option>
+                    <option value="PAM70">PAM70</option>
+                    <option value="PAM30">PAM30</option>
                 </param>
-                <when value="hmmer">
-                    <param name="database" type="select" label="HMM target database" help="Choose either the full eggNOG database or a subset of it. Contact your Galaxy admin to have additional HMM databases installed.">
-                        <options from_data_table="eggnog_mapper_hmm_dbs">
-                            <!--
-                            <filter type="param_value" ref="eggnog_data" column="1" />
-                            <filter type="unique_value" column="3" />
-                            <validator type="no_options" message="No HMM databases are available; request installation from your Galaxy admin." />
-                            -->
-                        </options>
+                <when value="BLOSUM90">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
+                        <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                        <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                        <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                        <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                        <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                        <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
                     </param>
-                    <conditional name="hmm_options">
-                        <param name="hmm_settings" type="select" label="HMM Search Options">
-                            <option value="default">Use defaults</option>
-                            <option value="specified">Set HMM Search Options</option>
-                        </param>
-                        <when value="default"/>
-                        <when value="specified">
-                            <param name="hmm_maxhits" type="integer" value="1" label="Max number of hits to report per query sequence"/>
-                            <param name="hmm_evalue" type="float" min="0" value="0.001" label="E-value threshold" />
-                            <param name="hmm_score" type="integer" min="0" value="20" label="Bit score threshold" />
-                            <param name="hmm_maxseqlen" type="integer" value="5000" label="Ignore query sequences larger than `maxseqlen`.  Default=5000" />
-                            <param name="hmm_qcov" type="float" value="" min="0." max="1." optional="true" label="min query coverage (from 0 to 1). Default=(disabled)" />
-                            <param name="Z" type="integer" value="40000000" min="0" label="Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases).  Default=40,000,000" />
-                        </when>
-                    </conditional>
+                </when>
+                <when value="BLOSUM80">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                        <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                        <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                        <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                        <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                        <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                    </param>
+                </when>
+                <when value="BLOSUM62">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 11 --gapextend 2">Existence: 11  Extension: 2</option>
+                        <option value="--gapopen 10 --gapextend 2">Existence: 10  Extension: 2</option>
+                        <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
+                        <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                        <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                        <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                        <option value="--gapopen 13 --gapextend 1">Existence: 13  Extension: 1</option>
+                        <option value="--gapopen 12 --gapextend 1">Existence: 12  Extension: 1</option>
+                        <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11  Extension: 1</option>
+                        <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
+                        <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                    </param>
                 </when>
-                <when value="diamond">
-                    <!-- db.database is used in diamond mode only to name outputs -->
-                    <param name="database" type="hidden" value="diamond"/>
-                    <conditional name="matrix_gapcosts">
-                        <param argument="--matrix" type="select" label="Scoring matrix and gap costs">
-                            <option value="BLOSUM90">BLOSUM90</option>
-                            <option value="BLOSUM80">BLOSUM80</option>
-                            <option value="BLOSUM62" selected="true">BLOSUM62</option>
-                            <option value="BLOSUM50">BLOSUM50</option>
-                            <option value="BLOSUM45">BLOSUM45</option>
-                            <option value="PAM250">PAM250</option>
-                            <option value="PAM70">PAM70</option>
-                            <option value="PAM30">PAM30</option>
-                        </param>
-                        <when value="BLOSUM90">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
-                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
-                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
-                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
-                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
-                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
-                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
-                            </param>
-                        </when>
-                        <when value="BLOSUM80">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
-                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
-                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
-                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
-                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
-                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
-                            </param>
-                        </when>
-                        <when value="BLOSUM62">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 11 --gapextend 2">Existence: 11  Extension: 2</option>
-                                <option value="--gapopen 10 --gapextend 2">Existence: 10  Extension: 2</option>
-                                <option value="--gapopen 9 --gapextend 2">Existence: 9  Extension: 2</option>
-                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
-                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
-                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
-                                <option value="--gapopen 13 --gapextend 1">Existence: 13  Extension: 1</option>
-                                <option value="--gapopen 12 --gapextend 1">Existence: 12  Extension: 1</option>
-                                <option value="--gapopen 11 --gapextend 1" selected="true">Existence: 11  Extension: 1</option>
-                                <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
-                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
-                            </param>
-                        </when>
-                        <when value="BLOSUM50">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
-                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
-                                <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
-                                <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
-                                <option value="--gapopen 9 --gapextend 3">Existence: 9  Extension: 3</option>
-                                <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
-                                <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
-                                <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
-                                <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13  Extension: 2</option>
-                                <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
-                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
-                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
-                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
-                                <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
-                                <option value="--gapopen 15 --gapextend 1">Existence: 15  Extension: 1</option>
-                            </param>
-                        </when>
-                        <when value="BLOSUM45">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
-                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
-                                <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
-                                <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
-                                <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15  Extension: 2</option>
-                                <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
-                                <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
-                                <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
-                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
-                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
-                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
-                                <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
-                            </param>
-                        </when>
-                        <when value="PAM250">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 15 --gapextend 3">Existence: 15  Extension: 3</option>
-                                <option value="--gapopen 14 --gapextend 3">Existence: 14  Extension: 3</option>
-                                <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
-                                <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
-                                <option value="--gapopen 17 --gapextend 2">Existence: 17  Extension: 2</option>
-                                <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
-                                <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
-                                <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14  Extension: 2</option>
-                                <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
-                                <option value="--gapopen 21 --gapextend 1">Existence: 21  Extension: 1</option>
-                                <option value="--gapopen 20 --gapextend 1">Existence: 20  Extension: 1</option>
-                                <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
-                                <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
-                                <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
-                            </param>
-                        </when>
-                        <when value="PAM70">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
-                                <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
-                                <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
-                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
-                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
-                                <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
-                                <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
-                                <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
-                            </param>
-                        </when>
-                        <when value="PAM30">
-                            <param name="gap_costs" type="select" label="Gap Costs">
-                                <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
-                                <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
-                                <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
-                                <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
-                                <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
-                                <option value="--gapopen 5 --gapextend 2">Existence: 5  Extension: 2</option>
-                                <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
-                                <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
-                                <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9  Extension: 1</option>
-                                <option value="--gapopen 8 --gapextend 1">Existence: 8  Extension: 1</option>
-                            </param>
-                        </when>
-                    </conditional>
+                <when value="BLOSUM50">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                        <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                        <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
+                        <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
+                        <option value="--gapopen 9 --gapextend 3">Existence: 9  Extension: 3</option>
+                        <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
+                        <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
+                        <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
+                        <option value="--gapopen 13 --gapextend 2" selected="true">Existence: 13  Extension: 2</option>
+                        <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
+                        <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                        <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                        <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                        <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
+                        <option value="--gapopen 15 --gapextend 1">Existence: 15  Extension: 1</option>
+                    </param>
+                </when>
+                <when value="BLOSUM45">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                        <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                        <option value="--gapopen 11 --gapextend 3">Existence: 11  Extension: 3</option>
+                        <option value="--gapopen 10 --gapextend 3">Existence: 10  Extension: 3</option>
+                        <option value="--gapopen 15 --gapextend 2" selected="true">Existence: 15  Extension: 2</option>
+                        <option value="--gapopen 14 --gapextend 2">Existence: 14  Extension: 2</option>
+                        <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
+                        <option value="--gapopen 12 --gapextend 2">Existence: 12  Extension: 2</option>
+                        <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                        <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                        <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                        <option value="--gapopen 16 --gapextend 1">Existence: 16  Extension: 1</option>
+                    </param>
+                </when>
+                <when value="PAM250">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 15 --gapextend 3">Existence: 15  Extension: 3</option>
+                        <option value="--gapopen 14 --gapextend 3">Existence: 14  Extension: 3</option>
+                        <option value="--gapopen 13 --gapextend 3">Existence: 13  Extension: 3</option>
+                        <option value="--gapopen 12 --gapextend 3">Existence: 12  Extension: 3</option>
+                        <option value="--gapopen 17 --gapextend 2">Existence: 17  Extension: 2</option>
+                        <option value="--gapopen 16 --gapextend 2">Existence: 16  Extension: 2</option>
+                        <option value="--gapopen 15 --gapextend 2">Existence: 15  Extension: 2</option>
+                        <option value="--gapopen 14 --gapextend 2" selected="true">Existence: 14  Extension: 2</option>
+                        <option value="--gapopen 13 --gapextend 2">Existence: 13  Extension: 2</option>
+                        <option value="--gapopen 21 --gapextend 1">Existence: 21  Extension: 1</option>
+                        <option value="--gapopen 20 --gapextend 1">Existence: 20  Extension: 1</option>
+                        <option value="--gapopen 19 --gapextend 1">Existence: 19  Extension: 1</option>
+                        <option value="--gapopen 18 --gapextend 1">Existence: 18  Extension: 1</option>
+                        <option value="--gapopen 17 --gapextend 1">Existence: 17  Extension: 1</option>
+                    </param>
+                </when>
+                <when value="PAM70">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 12 --gapextend 3">Existence: 12 Extension: 3</option>
+                        <option value="--gapopen 11 --gapextend 2">Existence: 11 Extension: 2</option>
+                        <option value="--gapopen 8 --gapextend 2">Existence: 8  Extension: 2</option>
+                        <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                        <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                        <option value="--gapopen 11 --gapextend 1">Existence: 11  Extension: 1</option>
+                        <option value="--gapopen 10 --gapextend 1" selected="true">Existence: 10  Extension: 1</option>
+                        <option value="--gapopen 9 --gapextend 1">Existence: 9  Extension: 1</option>
+                    </param>
+                </when>
+                <when value="PAM30">
+                    <param name="gap_costs" type="select" label="Gap Costs">
+                        <option value="--gapopen 15 --gapextend 3">Existence: 15 Extension: 3</option>
+                        <option value="--gapopen 13 --gapextend 3">Existence: 13 Extension: 3</option>
+                        <option value="--gapopen 14 --gapextend 2">Existence: 14 Extension: 2</option>
+                        <option value="--gapopen 7 --gapextend 2">Existence: 7  Extension: 2</option>
+                        <option value="--gapopen 6 --gapextend 2">Existence: 6  Extension: 2</option>
+                        <option value="--gapopen 5 --gapextend 2">Existence: 5  Extension: 2</option>
+                        <option value="--gapopen 14 --gapextend 1">Existence: 14 Extension: 1</option>
+                        <option value="--gapopen 10 --gapextend 1">Existence: 10  Extension: 1</option>
+                        <option value="--gapopen 9 --gapextend 1" selected="true">Existence: 9  Extension: 1</option>
+                        <option value="--gapopen 8 --gapextend 1">Existence: 8  Extension: 1</option>
+                    </param>
                 </when>
             </conditional>
+
+            <param name="query_cover" type="integer" value="0" min="0" max="100" label="Minimum query coverage" help="Report only alignments above the given percentage of query cover" />
+            <param name="subject_cover" type="integer" value="0" min="0" max="100" label="Minimum subject coverage" help="Report only alignments above the given percentage of subject cover" />
+        </section>
+
         <section name="annotation_options" expanded="false" title="Annotation Options">
-            <param name="tax_scope" type="select" optional="true" label="Set taxonomic scope">
-                <option value="NOG">All organisms  (NOG)</option>
-                <option value="aciNOG">Acidobacteria  (aciNOG)</option>
-                <option value="acidNOG">Acidobacteriia  (acidNOG)</option>
-                <option value="acoNOG">Aconoidasida  (acoNOG)</option>
-                <option value="actNOG">Actinobacteria  (actNOG)</option>
-                <option value="agaNOG">Agaricales  (agaNOG)</option>
-                <option value="agarNOG">Agaricomycetes  (agarNOG)</option>
-                <option value="apiNOG">Apicomplexa  (apiNOG)</option>
-                <option value="aproNOG">Proteobacteria_alpha  (aproNOG)</option>
-                <option value="aquNOG">Aquificae  (aquNOG)</option>
-                <option value="arNOG">Archaea  (arNOG)</option>
-                <option value="arcNOG">Archaeoglobi  (arcNOG)</option>
-                <option value="artNOG">Arthropoda  (artNOG)</option>
-                <option value="arthNOG">Arthrodermataceae  (arthNOG)</option>
-                <option value="ascNOG">Ascomycota  (ascNOG)</option>
-                <option value="aveNOG">Aves  (aveNOG)</option>
-                <option value="bacNOG">Bacilli  (bacNOG)</option>
-                <option value="bactNOG">Bacteria  (bactNOG)</option>
-                <option value="bacteNOG">Bacteroidia  (bacteNOG)</option>
-                <option value="basNOG">Basidiomycota  (basNOG)</option>
-                <option value="bctoNOG">Bacteroidetes  (bctoNOG)</option>
-                <option value="biNOG">Bilateria  (biNOG)</option>
-                <option value="bproNOG">Proteobacteria_beta  (bproNOG)</option>
-                <option value="braNOG">Brassicales  (braNOG)</option>
-                <option value="carNOG">Carnivora  (carNOG)</option>
-                <option value="chaNOG">Chaetomiaceae  (chaNOG)</option>
-                <option value="chlNOG">Chlorobi  (chlNOG)</option>
-                <option value="chlaNOG">Chlamydiae  (chlaNOG)</option>
-                <option value="chloNOG">Chloroflexi  (chloNOG)</option>
-                <option value="chlorNOG">Chloroflexi  (chlorNOG)</option>
-                <option value="chloroNOG">Chlorophyta  (chloroNOG)</option>
-                <option value="chorNOG">Chordata  (chorNOG)</option>
-                <option value="chrNOG">Chromadorea  (chrNOG)</option>
-                <option value="cloNOG">Clostridia  (cloNOG)</option>
-                <option value="cocNOG">Coccidia  (cocNOG)</option>
-                <option value="creNOG">Crenarchaeota  (creNOG)</option>
-                <option value="cryNOG">Cryptosporidiidae  (cryNOG)</option>
-                <option value="cyaNOG">Cyanobacteria  (cyaNOG)</option>
-                <option value="cytNOG">Cytophagia  (cytNOG)</option>
-                <option value="debNOG">Debaryomycetaceae  (debNOG)</option>
-                <option value="defNOG">Deferribacteres  (defNOG)</option>
-                <option value="dehNOG">Dehalococcoidetes  (dehNOG)</option>
-                <option value="deiNOG">Deinococcusthermus  (deiNOG)</option>
-                <option value="delNOG">delta/epsilon  (delNOG)</option>
-                <option value="dipNOG">Diptera  (dipNOG)</option>
-                <option value="dotNOG">Dothideomycetes  (dotNOG)</option>
-                <option value="dproNOG">Proteobacteria_delta  (dproNOG)</option>
-                <option value="droNOG">Drosophilidae  (droNOG)</option>
-                <option value="eproNOG">Proteobacteria_epsilon  (eproNOG)</option>
-                <option value="eryNOG">Erysipelotrichi  (eryNOG)</option>
-                <option value="euNOG">Eukaryotes  (euNOG)</option>
-                <option value="eurNOG">Euryarchaeota  (eurNOG)</option>
-                <option value="euroNOG">Eurotiomycetes  (euroNOG)</option>
-                <option value="eurotNOG">Eurotiales  (eurotNOG)</option>
-                <option value="fiNOG">Fishes  (fiNOG)</option>
-                <option value="firmNOG">Firmicutes  (firmNOG)</option>
-                <option value="flaNOG">Flavobacteriia  (flaNOG)</option>
-                <option value="fuNOG">Fungi  (fuNOG)</option>
-                <option value="fusoNOG">Fusobacteria  (fusoNOG)</option>
-                <option value="gproNOG">Proteobacteria_gamma  (gproNOG)</option>
-                <option value="haeNOG">Haemosporida  (haeNOG)</option>
-                <option value="halNOG">Halobacteria  (halNOG)</option>
-                <option value="homNOG">Hominidae  (homNOG)</option>
-                <option value="hymNOG">Hymenoptera  (hymNOG)</option>
-                <option value="hypNOG">Hypocreales  (hypNOG)</option>
-                <option value="inNOG">Insects  (inNOG)</option>
-                <option value="kinNOG">Kinetoplastida  (kinNOG)</option>
-                <option value="lepNOG">Lepidoptera  (lepNOG)</option>
-                <option value="lilNOG">Liliopsida  (lilNOG)</option>
-                <option value="maNOG">Mammals  (maNOG)</option>
-                <option value="magNOG">Magnaporthales  (magNOG)</option>
-                <option value="meNOG">Animals  (meNOG)</option>
-                <option value="metNOG">Methanobacteria  (metNOG)</option>
-                <option value="methNOG">Methanococci  (methNOG)</option>
-                <option value="methaNOG">Methanomicrobia  (methaNOG)</option>
-                <option value="necNOG">Nectriaceae  (necNOG)</option>
-                <option value="negNOG">Negativicutes  (negNOG)</option>
-                <option value="nemNOG">Nematodes  (nemNOG)</option>
-                <option value="onyNOG">Onygenales  (onyNOG)</option>
-                <option value="opiNOG">Opisthokonts  (opiNOG)</option>
-                <option value="perNOG">Peronosporales  (perNOG)</option>
-                <option value="plaNOG">Planctomycetes  (plaNOG)</option>
-                <option value="pleNOG">Pleosporales  (pleNOG)</option>
-                <option value="poaNOG">Poales  (poaNOG)</option>
-                <option value="prNOG">Primates  (prNOG)</option>
-                <option value="proNOG">Proteobacteria  (proNOG)</option>
-                <option value="rhaNOG">Rhabditida  (rhaNOG)</option>
-                <option value="roNOG">Rodents  (roNOG)</option>
-                <option value="sacNOG">Saccharomycetaceae  (sacNOG)</option>
-                <option value="saccNOG">Saccharomycetes  (saccNOG)</option>
-                <option value="sorNOG">Sordariales  (sorNOG)</option>
-                <option value="sordNOG">Sordariomycetes  (sordNOG)</option>
-                <option value="sphNOG">Sphingobacteriia  (sphNOG)</option>
-                <option value="spiNOG">Spirochaetes  (spiNOG)</option>
-                <option value="spriNOG">Supraprimates  (spriNOG)</option>
-                <option value="strNOG">Streptophyta  (strNOG)</option>
-                <option value="synNOG">Synergistetes  (synNOG)</option>
-                <option value="tenNOG">Tenericutes  (tenNOG)</option>
-                <option value="thaNOG">Thaumarchaeota  (thaNOG)</option>
-                <option value="theNOG">Thermoplasmata  (theNOG)</option>
-                <option value="therNOG">Thermotogae  (therNOG)</option>
-                <option value="thermNOG">Thermococci  (thermNOG)</option>
-                <option value="treNOG">Tremellales  (treNOG)</option>
-                <option value="veNOG">Vertebrates  (veNOG)</option>
-                <option value="verNOG">Verrucomicrobia  (verNOG)</option>
-                <option value="verrNOG">Verrucomicrobiae  (verrNOG)</option>
-                <option value="virNOG">Viridiplantae  (virNOG)</option>
-            </param>
+            <param name="tax_scope" type="integer" optional="true" label="Set taxonomic scope" help="NCBI taxonomy id" />
             <param name="target_orthologs" type="select" label="target orthologs for functional transfer">
                 <option value="one2one">one2one</option>
                 <option value="many2one">many2one</option>
@@ -348,13 +198,13 @@
         <section name="seed_ortholog_options" expanded="false" title="Seed Ortholog Search Options">
             <param name="seed_ortholog_evalue" type="float" value="0.001" min="0" label="Min E-value threshold">
                 <help>
-                Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches. 
+                Min E-value expected when searching for seed eggNOG ortholog. Applies to phmmer/diamond searches.
                 Queries not having a significant seed orthologs (E-value less than threshold) will not be annotated.
                 </help>
             </param>
             <param name="seed_ortholog_score" type="integer" value="60" min="0" label="Minimum bit score threshold">
                 <help>
-                Min bit score expected when searching for seed eggNOG ortholog. 
+                Min bit score expected when searching for seed eggNOG ortholog.
                 Queries not having a significant seed orthologs will not be annotated.
                 </help>
             </param>
@@ -369,24 +219,18 @@
         </section>
     </inputs>
     <outputs>
-        <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
+        <data name="seed_orthologs" format="tabular" label="${tool.name} on ${on_string}: seed_orthologs" from_work_dir="results.emapper.seed_orthologs">
             <actions>
                 <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score"/>
             </actions>
         </data>
-        <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations" from_work_dir="results.emapper.annotations">
+        <data name="annotations" format="tabular" label="${tool.name} on ${on_string}: annotations" from_work_dir="results.emapper.annotations">
             <filter>not output_options['no_annot']</filter>
             <actions>
-                <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_gene_name,GO_terms,KEGG_KO,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_HMM_model_annotation"/>
+                <action name="column_names" type="metadata" default="query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,predicted_taxonomic_group,predicted_protein_name,GO_terms,EC_number,KEGG_KO,KEGG_Pathway,KEGG_Module,KEGG_Reaction,KEGG_rclass,BRITE,KEGG_TC,CAZy,BiGG_Reactions,Annotation_tax_scope,Matching_OGs,best_OG|evalue|score,COG_functional_categories,eggNOG_free_text_description"/>
             </actions>
         </data>
-        <data name="hmm_hits" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.hmm_hits"  from_work_dir="results.emapper.hmm_hits">
-            <filter>db['mode'] == 'hmmer'</filter>
-            <actions>
-                <action name="column_names" type="metadata" default="query_name,hit,evalue,sum_score,query_length,hmmfrom,hmmto,seqfrom,seqto,query_coverage"/>
-            </actions>
-        </data>
-        <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: ${db.database}.annotations.orthologs"  from_work_dir="results.emapper.annotations.orthologs">
+        <data name="annotations_orthologs" format="tabular" label="${tool.name} on ${on_string}: annotations.orthologs"  from_work_dir="results.emapper.annotations.orthologs">
             <filter>output_options['report_orthologs']</filter>
             <actions>
                 <action name="column_names" type="metadata" default="query_name,orthologs"/>
@@ -395,23 +239,32 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
-            <param name="database" value="ENOG411CB2I"/>
-            <param name="mode" value="hmmer"/>
-            <!--
-            <param name="test" value="true"/>
-            -->
-            <param name="eggnog_data" value="4.5"/>
+            <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
+            <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/>
             <param name="no_annot" value="true"/>
             <param name="no_file_comments" value="true"/>
-            <output name="hmm_hits" file="HMM_nlim.emapper.hmm_hits" ftype="tabular"/>
+            <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
         </test>
         <test>
-            <param name="input" value="nlim_fragment.fasta" ftype="fasta"/>
-            <param name="eggnog_data" value="4.5"/> <!-- not passed in test, but required for test to work -->
-            <param name="no_annot" value="true"/>
-            <param name="mode" value="diamond"/>
+            <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
+            <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
+            <param name="report_orthologs" value="true"/>
+            <param name="no_file_comments" value="true"/>
             <output name="seed_orthologs" file="DIA_nlim.emapper.seed_orthologs" ftype="tabular"/>
+            <output name="annotations" file="DIA_nlim.emapper.annotations" ftype="tabular"/>
+            <output name="annotations_orthologs" file="DIA_nlim.emapper.annotations_orthologs" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="Nmar_0135.fa" ftype="fasta"/>
+            <param name="eggnog_data" value="@EGGNOG_DB_VERSION@"/> <!-- not passed in test, but required for test to work -->
+            <param name="report_orthologs" value="true"/>
+            <param name="no_file_comments" value="true"/>
+            <section name="annotation_options">
+                <param name="tax_scope" value="651137" />
+            </section>
+            <output name="seed_orthologs" file="scoped.emapper.seed_orthologs" ftype="tabular"/>
+            <output name="annotations" file="scoped.emapper.annotations" ftype="tabular"/>
+            <output name="annotations_orthologs" file="scoped.emapper.annotations_orthologs" ftype="tabular"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -421,38 +274,22 @@
 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, 
+``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>`_.
 
-Options
--------
-
-``eggnog-mapper`` can use two search algorithms: `HMMER <http://hmmer.org/>`_ and `DIAMOND <https://github.com/bbuchfink/diamond>`_. 
-HMMER is more sensitive, while DIAMOND is faster and useful for larger sets of query sequences. 
-
-
 Outputs
 -------
 
-**hmm_hits**
-
-For each query sequence, a list of significant 
-hits to eggNOG Orthologous Groups (OGs) is reported. 
-Each line in the file represents a hit, where evalue, bit-score, 
-query-coverage and the sequence coordinates of the match are reported. 
-If multiple hits exist for a given query, results are sorted by e-value.
-Only returned when using HMMER mode. 
-
 **seed_orthologs**
 
-each line in the file provides the best match of each query within the best Orthologous Group (OG) 
-reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG. 
-The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG. 
-If using the diamond search mode, seed orthologs are directly 
+each line in the file provides the best match of each query within the best Orthologous Group (OG)
+reported in the [project].hmm_hits file, obtained running PHMMER against all sequences within the best OG.
+The seed ortholog is used to fetch fine-grained orthology relationships from eggNOG.
+If using the diamond search mode, seed orthologs are directly
 obtained from the best matching sequences by running DIAMOND against the whole eggNOG protein space.
 
 **annotations**
@@ -463,14 +300,24 @@
 - ``seed_eggNOG_ortholog``: best protein match in eggNOG
 - ``seed_ortholog_evalue``: best protein match (e-value)
 - ``seed_ortholog_score``: best protein match (bit-score)
-- ``predicted_gene_name``: Predicted gene name for query sequences
+- ``predicted_taxonomic_group``
+- ``predicted_protein_name``: Predicted protein name for query sequences
 - ``GO_terms``: Comma delimited list of predicted Gene Ontology terms
-- ``KEGG_pathways``: Comma delimited list of predicted KEGG pathways
+- ``EC_number``
+- ``KEGG_KO``
+- ``KEGG_Pathway``: Comma delimited list of predicted KEGG pathways
+- ``KEGG_Module``
+- ``KEGG_Reaction``
+- ``KEGG_rclass``
+- ``BRITE``
+- ``KEGG_TC``
+- ``CAZy``
+- ``BiGG_Reactions``
 - ``Annotation_tax_scope``: The taxonomic scope used to annotate this query sequence
 - ``Matching_OGs``: Comma delimited list of matching eggNOG Orthologous Groups
-- ``best_OG|evalue|score``: Best matching Orthologous Groups (only in HMM mode)
-- ``COG functional categories``: COG functional category inferred from best matching OG
-- ``eggNOG_HMM_model_annotation``: eggNOG functional description inferred from best matching OG
+- ``best_OG|evalue|score``: Best matching Orthologous Groups (deprecated, use smallest from eggnog OGs)
+- ``COG_functional_categories``: COG functional category inferred from best matching OG
+- ``eggNOG_free_text_description``
 
     ]]></help>
     <expand macro="citations"/>