# HG changeset patch # User galaxyp # Date 1658243692 0 # Node ID 9d1fbff733cfbc64fb3538e8c604517d9f43cedb # Parent 5a30ae278db0c5dca0a137bde4657d60cc7c5432 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd diff -r 5a30ae278db0 -r 9d1fbff733cf eggnog_macros.xml --- 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 @@ 2.1.8 - 2.1.8 + 3 5.0.2 + + + + + + + + query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 5a30ae278db0 -r 9d1fbff733cf eggnog_mapper.xml --- a/eggnog_mapper.xml Mon Jun 20 12:49:52 2022 +0000 +++ b/eggnog_mapper.xml Tue Jul 19 15:14:52 2022 +0000 @@ -6,370 +6,472 @@ annotate_hits_table.tsv + && #end if - ## Diamond option - #if $seed_ortho_options.ortho_method.m == "diamond": - --matrix '$seed_ortho_options.ortho_method.matrix_gapcosts.matrix' - $seed_ortho_options.ortho_method.matrix_gapcosts.gap_costs - --sensmode $seed_ortho_options.ortho_method.sensmode - $seed_ortho_options.ortho_method.dmnd_iterate - $seed_ortho_options.ortho_method.dmnd_ignore_warnings - #elif $seed_ortho_options.ortho_method.m == "mmseqs": - --start_sens $seed_ortho_options.ortho_method.start_sens - --sens_steps $seed_ortho_options.ortho_method.sens_steps - --final_sens $seed_ortho_options.ortho_method.final_sens + emapper.py + --data_dir '$eggnog_data.fields.path' + -m '$ortho_method.m' + + #if $ortho_method.m in ['diamond', 'mmseqs', 'cache']: + -i '$ortho_method.input' + --itype '$ortho_method.input_trans.itype' + #if $ortho_method.input_trans.itype in ['CDS', 'genome', 'metagenome']: + $ortho_method.input_trans.translate + #end if + #if $ortho_method.input_trans.itype in ['genome', 'metagenome']: + --genepred $ortho_method.input_trans.genepred + #end if + #elif $ortho_method.m == "no_search" + --annotate_hits_table annotate_hits_table.tsv #end if - - ## Common options for search filtering - #if $seed_ortho_options.query_cover: - --query_cover $seed_ortho_options.query_cover - #end if - #if $seed_ortho_options.subject_cover: - --subject_cover $seed_ortho_options.subject_cover - #end if - #if $seed_ortho_options.pident: - --pident $seed_ortho_options.pident + + #if $ortho_method.m == 'cache' + --cache '$ortho_method.cache' #end if - #if $annotation_options.tax_scope: - --tax_scope=$annotation_options.tax_scope - #end if - #if $annotation_options.target_orthologs: - --target_orthologs=$annotation_options.target_orthologs + #if $ortho_method.m in ['diamond', 'mmseqs']: + ## Diamond option + #if $ortho_method.m == "diamond": + --matrix '$ortho_method.matrix_gapcosts.matrix' + $ortho_method.matrix_gapcosts.gap_costs + --sensmode $ortho_method.sensmode + $ortho_method.dmnd_iterate + $ortho_method.dmnd_ignore_warnings + #elif $ortho_method.m == "mmseqs": + --start_sens $ortho_method.start_sens + --sens_steps $ortho_method.sens_steps + --final_sens $ortho_method.final_sens + #end if + + ## Common options for search filtering (applies to diamond and mmseqs only) + #if str($ortho_method.query_cover): + --query_cover $ortho_method.query_cover + #end if + #if str($ortho_method.subject_cover): + --subject_cover $ortho_method.subject_cover + #end if + #if str($ortho_method.pident): + --pident $ortho_method.pident + #end if + #if str($ortho_method.evalue): + --evalue $ortho_method.evalue + #end if + #if str($ortho_method.score): + --score $ortho_method.score + #end if #end if - #if $annotation_options.go_evidence: - --go_evidence=$annotation_options.go_evidence - #end if - #if $seed_ortholog_options.seed_ortholog_evalue: - --evalue=$seed_ortholog_options.seed_ortholog_evalue - #end if - #if str($seed_ortholog_options.seed_ortholog_score): - --score=$seed_ortholog_options.seed_ortholog_score + + #if $annotation_options.no_annot == "--no_annot" + --no_annot + #else + #if str($annotation_options.seed_ortholog_evalue): + --seed_ortholog_evalue $annotation_options.seed_ortholog_evalue + #end if + #if str($annotation_options.seed_ortholog_score): + --seed_ortholog_score $annotation_options.seed_ortholog_score + #end if + #if $annotation_options.tax_scope: + --tax_scope=$annotation_options.tax_scope + #end if + #if $annotation_options.target_orthologs: + --target_orthologs=$annotation_options.target_orthologs + #end if + #if $annotation_options.go_evidence: + --go_evidence=$annotation_options.go_evidence + #end if #end if $output_options.no_file_comments - $output_options.no_annot $output_options.report_orthologs + $output_options.md5 --output='results' - -i '${input}' --cpu "\${GALAXY_SLOTS:-4}" + --scratch_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} + --temp_dir \${TEMP:-\$_GALAXY_JOB_TMP_DIR} ]]> - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + value.metadata.columns == 11 + + + + + + + value.metadata.columns == 22 + + + + - - - -
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- - - 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. - - - - - Min bit score expected when searching for seed eggNOG ortholog. - Queries not having a significant seed orthologs will not be annotated. - - -
+ + + + 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. + + + + + Min bit score expected when searching for seed eggNOG ortholog. + Queries not having a significant seed orthologs will not be annotated. + + + + + + + + + + + + + + + + + + +
- - - +
+ ortho_method['m'] not in ['no_search', 'cache'] - + - not output_options['no_annot'] + annotation_options['no_annot'] == '' - + + + + + + + + - output_options['report_orthologs'] + ortho_method['m'] != 'cache' and output_options['report_orthologs'] + + ortho_method['m'] == 'cache' and output_options['output_no_annotations'] + + - - - - + + + + + + +
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