# HG changeset patch
# User iuc
# Date 1633376264 0
# Node ID 1a59958c1f7620141a0b141644babde94a5e657f
# Parent 40b87aef52414c02f6eaea4841c4d29d2881ddce
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"
diff -r 40b87aef5241 -r 1a59958c1f76 funannotate_predict.xml
--- a/funannotate_predict.xml Thu Aug 26 06:55:33 2021 +0000
+++ b/funannotate_predict.xml Mon Oct 04 19:37:44 2021 +0000
@@ -32,6 +32,8 @@
--database '$database.fields.path'
#end if
+$force
+
--species '${organism.species}'
--isolate '${organism.isolate}'
--strain '${organism.strain}'
@@ -46,7 +48,7 @@
--parameters '${parameters}'
#end if
-#if $evidences.rna_bam:
+#if $evidences.rna_bam
--rna_bam ${evidences.rna_bam}
#end if
@@ -71,6 +73,9 @@
--p2g_pident ${evidences.p2g_pident}
--p2g_prefilter ${evidences.p2g_prefilter}
+--busco_seed_species '${busco.busco_seed_species}'
+--busco_db '${busco.busco_db}'
+
#if $augustus.augustus_species != 'none':
--augustus_species '${augustus.augustus_species}'
#end if
@@ -85,9 +90,6 @@
--soft_mask ${genemark.soft_mask}
#end if
---busco_seed_species '${busco.busco_seed_species}'
---busco_db '${busco.busco_db}'
-
$evm.repeats2evm
#if $evm.evm_partitioning.evm_partition == "yes":
--evm-partition-interval ${evm.evm_partitioning.evm_partition_interval}
@@ -145,6 +147,8 @@
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@@ -199,7 +216,7 @@
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+ outputs and 'gbk' in outputs
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+ outputs and 'tbl' in outputs
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+ outputs and 'gff3' in outputs
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+ outputs and 'proteins_fa' in outputs
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+ outputs and 'mrna_transcripts_fa' in outputs
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+ outputs and 'cds_transcripts_fa' in outputs
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+ outputs and 'tbl2asn_report' in outputs
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+ outputs and 'tbl2asn_error' in outputs
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+ outputs and 'tbl2asn_validation' in outputs
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+ outputs and 'stats' in outputs
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@@ -271,16 +308,17 @@
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