Mercurial > repos > galaxyp > eggnog_mapper
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 |
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--- 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"/>