# HG changeset patch
# User galaxyp
# Date 1658243651 0
# Node ID 1f2be4ae431fe11033c09e2232a0227ae330e946
# Parent 3d30526975d79a7dfbab7f9e25cdb3394ab56153
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper commit 07877ba6d3fb6e28e94500f2392db6393cf325fd
diff -r 3d30526975d7 -r 1f2be4ae431f eggnog_macros.xml
--- a/eggnog_macros.xml Mon Jun 20 12:48:22 2022 +0000
+++ b/eggnog_macros.xml Tue Jul 19 15:14:11 2022 +0000
@@ -1,7 +1,7 @@
2.1.8
- 2.1.8
+ 3
5.0.2
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+ query_name,seed_eggNOG_ortholog,seed_ortholog_evalue,seed_ortholog_score,query_start,query_end,seed_start,seed_end,pident,query_cov,seed_cov
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diff -r 3d30526975d7 -r 1f2be4ae431f eggnog_mapper.xml
--- a/eggnog_mapper.xml Mon Jun 20 12:48:22 2022 +0000
+++ b/eggnog_mapper.xml Tue Jul 19 15:14:11 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}
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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.
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- Min bit score expected when searching for seed eggNOG ortholog.
- Queries not having a significant seed orthologs will not be annotated.
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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.
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+ Min bit score expected when searching for seed eggNOG ortholog.
+ Queries not having a significant seed orthologs will not be annotated.
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+ ortho_method['m'] not in ['no_search', 'cache']
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- not output_options['no_annot']
+ annotation_options['no_annot'] == ''
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- output_options['report_orthologs']
+ ortho_method['m'] != 'cache' and output_options['report_orthologs']
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+ ortho_method['m'] == 'cache' and output_options['output_no_annotations']
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