# HG changeset patch
# User iuc
# Date 1758030723 0
# Node ID d4134260b442817c61298a58a129f62378606b9e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap commit d966ed462a49d1949345717ae4fdb685c6a1450a
diff -r 000000000000 -r d4134260b442 lexicmap-index.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lexicmap-index.xml Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,81 @@
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+ Builds LexicMap index
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+ macros.xml
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+ fasta_list.tsv &&
+mkdir '$lexicmap_index.extra_files_path' &&
+lexicmap index
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+ --threads "\${GALAXY_SLOTS:-1}"
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+ -X ./fasta_list.tsv -O '$lexicmap_index.extra_files_path'
+ --big-genomes '$lexicmap_big_genomes'
+ --batch-size '$batch_size'
+ --contig-interval '$contig_interval'
+ --kmer '$kmer'
+ --masks '$masks'
+ --max-genome '$max_genome'
+ --min-seq-len '$min_seq_len'
+ --rand-seed '$rand_seed'
+ --seed-in-desert-dist '$seed_in_desert_dist'
+ --seed-max-desert '$seed_max_desert'
+ #if $mask_file
+ --mask-file '$mask_file'
+ #end if
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+ ]]>
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diff -r 000000000000 -r d4134260b442 lexicmap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lexicmap.xml Tue Sep 16 13:52:03 2025 +0000
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+ nucleotide sequence tool for querying genomes
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+ macros.xml
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\ No newline at end of file
diff -r 000000000000 -r d4134260b442 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,45 @@
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+ 0.7.0
+ 0
+ 25.0
+ fasta.gz,fasta
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+ lexicmap
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+ lexicmap
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+ 10.1101/2024.08.30.610459
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diff -r 000000000000 -r d4134260b442 test-data/db.lmi/genomes.chunks.bin
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/genomes.map.bin
Binary file test-data/db.lmi/genomes.map.bin has changed
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/genomes/batch_0000/genomes.bin
Binary file test-data/db.lmi/genomes/batch_0000/genomes.bin has changed
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/genomes/batch_0000/genomes.bin.idx
Binary file test-data/db.lmi/genomes/batch_0000/genomes.bin.idx has changed
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/info.toml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/db.lmi/info.toml Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,24 @@
+# Index format
+main-version = 3
+minor-version = 4
+# LexicHash
+max-K = 31
+masks = 20000
+rand-seed = 1
+# Seed distance
+max-seed-dist = 100
+seed-dist-in-desert = 50
+# Seeds (k-mer-value data) files
+chunks = 2
+index-partitions = 4096
+# Input genomes
+input-genomes = 1
+# Input bases
+input-bases = 7417
+# Genome data.
+# 'genomes' might be larger than 'input-genomes', as some big fragmented genomes are split into multiple chunks.
+# In this case, 'genome-batch-size' is not accurate, being variable in different batches.
+genomes = 1
+genome-batch-size = 1
+genome-batches = 1
+contig-interval = 1000
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/masks.bin
Binary file test-data/db.lmi/masks.bin has changed
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/seeds/chunk_000.bin
Binary file test-data/db.lmi/seeds/chunk_000.bin has changed
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/seeds/chunk_000.bin.idx
Binary file test-data/db.lmi/seeds/chunk_000.bin.idx has changed
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/seeds/chunk_001.bin
Binary file test-data/db.lmi/seeds/chunk_001.bin has changed
diff -r 000000000000 -r d4134260b442 test-data/db.lmi/seeds/chunk_001.bin.idx
Binary file test-data/db.lmi/seeds/chunk_001.bin.idx has changed
diff -r 000000000000 -r d4134260b442 test-data/genomes/GCF_001502155.1_ViralProj307776_genomic.fna.gz
Binary file test-data/genomes/GCF_001502155.1_ViralProj307776_genomic.fna.gz has changed
diff -r 000000000000 -r d4134260b442 test-data/genomes/GCF_001502175.1_ViralProj307780_genomic.fna.gz
Binary file test-data/genomes/GCF_001502175.1_ViralProj307780_genomic.fna.gz has changed
diff -r 000000000000 -r d4134260b442 test-data/lexicmap_big_genomes.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lexicmap_big_genomes.tsv Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,1 @@
+/[A-Za-z0-9_/]*/[A-Za-z0-9/_-]*\.dat too_large_genome
diff -r 000000000000 -r d4134260b442 test-data/lexicmap_index.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lexicmap_index.loc Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,4 @@
+# This file is just a placeholder since Galxy does
+# not yet suppoort uploading a lexicmap index, which
+# is required for functional tests.
+LexicMapIndex1 LexicMapIndex1 ${__HERE__}/db.lmi
\ No newline at end of file
diff -r 000000000000 -r d4134260b442 test-data/lexicmap_query.fasta.gz
Binary file test-data/lexicmap_query.fasta.gz has changed
diff -r 000000000000 -r d4134260b442 test-data/lexicmap_query_result.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lexicmap_query_result.tsv Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,2 @@
+query qlen hits sgenome sseqid qcovGnm cls hsp qcovHSP alenHSP pident gaps qstart qend sstart send sstr slen evalue bitscore
+query1 240 1 dataset_963f49fd-cb75-4b60-909c-e63a9651ba65 NC_028981.1 100.000 1 1 100.000 240 100.000 0 1 240 2001 2240 + 7417 3.76e-125 434
diff -r 000000000000 -r d4134260b442 tool-data/lexicmap_index.loc.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lexicmap_index.loc.xml Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,6 @@
+
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diff -r 000000000000 -r d4134260b442 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,6 @@
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diff -r 000000000000 -r d4134260b442 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Sep 16 13:52:03 2025 +0000
@@ -0,0 +1,6 @@
+
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