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samestr DB builder: probe for the mOTUs db_mOTU directory (+galaxy4) #8346

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samestr DB builder: probe for the mOTUs db_mOTU directory (+galaxy4) #8346

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2 changes: 1 addition & 1 deletion data_managers/data_manager_samestr_db/data_manager/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">1.2025.111</token>
<token name="@VERSION_SUFFIX@">3</token>
<token name="@VERSION_SUFFIX@">4</token>
<token name="@PROFILE@">25.0</token>


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15 changes: 9 additions & 6 deletions data_managers/data_manager_samestr_db/data_manager/samestr_db.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,17 +55,20 @@
#set $samestr_db_dir = $out_file.extra_files_path + '/samestr_db/' + $db_value
mkdir -p '$samestr_db_dir' &&

#set $markers_info1 = $db_path + '/db_mOTU/db_mOTU_taxonomy_ref-mOTUs.tsv'
#set $markers_info2 = $db_path + '/db_mOTU/db_mOTU_taxonomy_meta-mOTUs.tsv'
#set $markers_fasta = $db_path + '/db_mOTU/db_mOTU_DB_CEN.fasta'
## The motus_db_versioned 'path' may point either at the db_mOTU
## directory itself (the mOTUs DM value_translation targets
## motus_database/<value>/db_mOTU) or at its parent. Probe for a
## nested db_mOTU/ and normalize, matching the mOTUs profiler wrapper.
motus_db_dir='$db_path' &&
if [ -d "\$motus_db_dir/db_mOTU" ]; then motus_db_dir="\$motus_db_dir/db_mOTU"; fi &&

#set $db_version_file = $samestr_db_dir + '/' + $version_file_name
cp '$db_path'/db_mOTU/db_mOTU_versions '$db_version_file' &&
cp "\$motus_db_dir/db_mOTU_versions" '$db_version_file' &&


samestr db
--markers-info '$markers_info1' '$markers_info2'
--markers-fasta '$markers_fasta'
--markers-info "\$motus_db_dir/db_mOTU_taxonomy_ref-mOTUs.tsv" "\$motus_db_dir/db_mOTU_taxonomy_meta-mOTUs.tsv"
--markers-fasta "\$motus_db_dir/db_mOTU_DB_CEN.fasta"
--db-version '$db_version_file'
--output-dir '$samestr_db_dir'
&&
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