From 7686c033edb974379f855d2563149d56920f063e Mon Sep 17 00:00:00 2001 From: Rlibouban <127295521+rlibouba@users.noreply.github.com> Date: Thu, 13 Jul 2023 11:15:31 +0200 Subject: [PATCH] Miniprot Update version v0.10 to v0.12 (#5317) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update version * Add test for the new param * Update tools/miniprot/miniprot.xml Co-authored-by: Anthony Bretaudeau * Missing value * Modification param * Modification test for new param * Test * Add new test * Tests * New test * Comment added for trans parameter * Modification input section - trans param * modifications * Modications tests * Add new version 0.12 and news options * style fixes --------- Co-authored-by: Anthony Bretaudeau Co-authored-by: Björn Grüning --- tools/miniprot/macros.xml | 2 +- tools/miniprot/miniprot.xml | 229 ++- tools/miniprot/test-data/output_no_cs.gff | 1308 +++++++++++++ tools/miniprot/test-data/output_no_cs.gtf | 1522 +++++++++++++++ tools/miniprot/test-data/output_no_cs.paf | 325 +++ tools/miniprot/test-data/output_trans.gff | 1633 ++++++++++++++++ tools/miniprot/test-data/output_trans.gtf | 2172 +++++++++++++++++++++ tools/miniprot/test-data/output_trans.paf | 650 ++++++ 8 files changed, 7790 insertions(+), 51 deletions(-) create mode 100644 tools/miniprot/test-data/output_no_cs.gff create mode 100644 tools/miniprot/test-data/output_no_cs.gtf create mode 100644 tools/miniprot/test-data/output_no_cs.paf create mode 100644 tools/miniprot/test-data/output_trans.gff create mode 100644 tools/miniprot/test-data/output_trans.gtf create mode 100644 tools/miniprot/test-data/output_trans.paf diff --git a/tools/miniprot/macros.xml b/tools/miniprot/macros.xml index 44748209a1e..3c33e93db1a 100644 --- a/tools/miniprot/macros.xml +++ b/tools/miniprot/macros.xml @@ -1,5 +1,5 @@ - 0.10 + 0.12 10.1093/bioinformatics/btad014 diff --git a/tools/miniprot/miniprot.xml b/tools/miniprot/miniprot.xml index 60b2d594615..2b3ec7f2083 100644 --- a/tools/miniprot/miniprot.xml +++ b/tools/miniprot/miniprot.xml @@ -30,7 +30,7 @@ #if str($adv.mapping.intron_size.mode) == 'manual' -G $adv.mapping.intron_size.max_intron #elif str($adv.mapping.intron_size.mode) == 'auto' - -I + -I #end if #if str($adv.output.prefix) != 'MP' @@ -40,6 +40,8 @@ --outn=$adv.output.outputs_per_query --outc=$adv.output.output_fraction_query --outs=$adv.output.output_score_least + $adv.output.output_translated_protein + $adv.output.output_no_cs $adv.output.output_residue_alignment #end if #if str($db.dbtype) == 'fasta' @@ -58,6 +60,7 @@ #end if '$protein_fasta' > '$output_alignment' ]]> + @@ -65,19 +68,19 @@ - - - - - + + + + + - + - - + + @@ -89,34 +92,34 @@
- - - - - - - - - + + + + + + + + + - + - +
- - - - - - - + + + + + + + @@ -131,14 +134,15 @@ - - + + - - + + + +
- +
@@ -147,7 +151,7 @@ - + @@ -156,40 +160,40 @@ - + - + - - + + - - + + - - + + - + - + - + - + @@ -197,7 +201,6 @@ - @@ -212,13 +215,139 @@ - + + + + + + + + + + + + + +
+ +
+
+ + + + + + + +
+ + + + + + + + + +
+ +
+
+ + + + + + + + +
+ + + + + + + + + +
+ +
+
+ + + + + + + + +
+ + + + + + + + + +
+ +
+
+ + + + + + + +
+ + + + + + + + + +
+ +
+
+ + + + + + + +
+ + + + + + + + + +
+ +
+
+ + + +
- - +