# HG changeset patch
# User galaxytrakr
# Date 1789415225 0
# Node ID dd206296acbf2f502ce3d81173224c29394a8c9b
# Parent  e6b5e7a0d7e7f6ab29a441ca9d6a7290db1aa8ac
planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a

diff -r e6b5e7a0d7e7 -r dd206296acbf Dockerfile
--- a/Dockerfile	Fri Sep 11 22:01:39 2026 +0000
+++ b/Dockerfile	Mon Sep 14 19:47:05 2026 +0000
@@ -37,10 +37,10 @@
 
 WORKDIR /opt/mitokmer2
 
-# Compile the C++ read-screening program
-# kmer_read_1.cpp -> kmerread
-RUN g++ -O3 kmer_read_1.cpp -o kmerread -lz && \
-    chmod +x kmerread
+# Compile kmer_read_1.cpp -> kmerread7
+# kmer_read_m7.py calls ./kmerread7 as a subprocess
+RUN g++ -O3 kmer_read_1.cpp -o kmerread7 -lz && \
+    chmod +x kmerread7
 
 # Install any Python requirements declared in the repo
 RUN if [ -f requirements.txt ]; then \
@@ -64,22 +64,25 @@
     && rm -rf /var/lib/apt/lists/*
 
 # Copy compiled binary from build stage
-COPY --from=build /opt/mitokmer2/kmerread /usr/local/bin/kmerread
+# kmerread7 is called by kmer_read_m7.py as ./kmerread7 so it
+# must be in the working directory at runtime; place it in both
+# /usr/local/bin (for PATH) and /opt/mitokmer2 (for relative invocation)
+COPY --from=build /opt/mitokmer2/kmerread7 /usr/local/bin/kmerread7
+COPY --from=build /opt/mitokmer2/kmerread7 /opt/mitokmer2/kmerread7
 
 # Copy Python scripts and supporting files from build stage
 COPY --from=build /opt/mitokmer2 /opt/mitokmer2
 
 # Copy Python virtual environment from build stage
-# --copies in the build stage ensures no broken symlinks here
 COPY --from=build /opt/venv /opt/venv
 
-# Refresh the dynamic linker cache so zlib and other shared
-# libraries are found at runtime
+# Refresh the dynamic linker cache
 RUN ldconfig || true
 
 # Ensure all users (including arbitrary Galaxy UIDs) can
 # read and execute binaries, scripts, and the venv
-RUN chmod a+rx  /usr/local/bin/kmerread && \
+RUN chmod a+rx  /usr/local/bin/kmerread7 \
+                /opt/mitokmer2/kmerread7 && \
     chmod -R a+rX /opt/mitokmer2 && \
     chmod -R a+rX /opt/venv
 
diff -r e6b5e7a0d7e7 -r dd206296acbf mitokmer.xml
--- a/mitokmer.xml	Fri Sep 11 22:01:39 2026 +0000
+++ b/mitokmer.xml	Mon Sep 14 19:47:05 2026 +0000
@@ -5,41 +5,44 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        ## ── kmerread expects files at specific relative paths ─────────────────
-        ## ./mitoch/mitoch_probes.txt.gz  - probe database
-        ## ./jobs1/jobs1.txt              - jobs file listing sample reads
-        ## It is invoked with no arguments: ./kmerread
-        mkdir -p ./mitoch ./jobs1 ./reads &&
+        ## ── All paths are hardcoded in kmer_read_m7.py: ──────────────────────
+        ##   database:  ./mitochondria7/<multiple .txt files>
+        ##   jobs file: ./jobs7m/jobs7m.txt
+        ##   output:    ./jobs7m/jobs7m.csv
+        ##   binary:    ./kmerread7  (called as subprocess by the Python script)
+        mkdir -p ./mitochondria7 ./jobs7m &&
+
+        ## ── Link database files from the data table directory ─────────────────
+        ## The data table path points to a directory containing all the
+        ## mitochondria7 .txt files; symlink each one into ./mitochondria7/
+        ln -sf '${probe_db.fields.path}'/* ./mitochondria7/ &&
 
-        ## ── Link probe database to the path kmerread expects ─────────────────
-        ln -sf '${probe_db.fields.path}' ./mitoch/mitoch_probes.txt.gz &&
+        ## ── Symlink kmerread7 into the working directory ──────────────────────
+        ## kmer_read_m7.py calls ./kmerread7 (relative path), so it must exist
+        ## in the Galaxy job working directory
+        ln -sf /usr/local/bin/kmerread7 ./kmerread7 &&
 
-        ## ── Stage input reads ─────────────────────────────────────────────────
+        ## ── Write the jobs file ───────────────────────────────────────────────
+        ## Format: sample_name  num_files
+        ##         /abs/path/to/read1
+        ##         /abs/path/to/read2  ...
+        #set sample_name = $reads[0].element_identifier.replace(' ', '_').split('_')[:-1] | join('_')
+        printf '${sample_name}\t${reads|length}\n' > ./jobs7m/jobs7m.txt &&
         #for read in $reads
-            ln -sf '${read}' ./reads/${read.element_identifier.replace(' ', '_')} &&
+            printf '${read.file_name}\n' >> ./jobs7m/jobs7m.txt &&
         #end for
 
-        ## ── Write the jobs file in the format kmerread expects ───────────────
-        ## Line 1: <sample_name> <number_of_files>
-        ## Lines 2+: absolute path to each read file, one per line
-        #set sample_name = $reads[0].element_identifier.replace(' ', '_').split('_')[:-1] | join('_')
-        echo "${sample_name} ${reads|length}" > ./jobs1/jobs1.txt &&
-        #for read in $reads
-            echo "\$PWD/reads/${read.element_identifier.replace(' ', '_')}" >> ./jobs1/jobs1.txt &&
-        #end for
+        ## ── Run the Python orchestrator (no arguments) ────────────────────────
+        ## kmer_read_m7.py reads jobs7m/jobs7m.txt, calls ./kmerread7,
+        ## and writes results to jobs7m/jobs7m.csv
+        python3 /opt/mitokmer2/kmer_read_m7.py &&
 
-        ## ── Run kmerread (reads jobs1/jobs1.txt and mitoch/mitoch_probes.txt.gz
-        ##    by convention; no CLI arguments) ──────────────────────────────────
-        kmerread &&
-
-        ## ── Summarise results into CSV ────────────────────────────────────────
-        python3 /opt/mitokmer2/kmer_read_m7.py
-            -i ./jobs1
-            -o '${results_csv}'
+        ## ── Copy output CSV to Galaxy output path ─────────────────────────────
+        cp ./jobs7m/jobs7m.csv '${results_csv}'
     ]]></command>
 
     <inputs>
-        <!-- Probe database selected from Galaxy data table -->
+        <!-- Probe database directory selected from Galaxy data table -->
         <param name="probe_db"
                type="select"
                label="Mitochondrial k-mer probe database"
@@ -107,7 +110,8 @@
 **Mitochondrial k-mer probe database**
     Select a pre-installed probe database from the dropdown.  Databases are
     managed by your Galaxy administrator and registered in the
-    ``mitokmer_probe_db`` data table.
+    ``mitokmer_probe_db`` data table.  The database consists of a directory
+    of supporting ``.txt`` files.
 
 **Input reads**
     One or more FASTQ or FASTA files (gzipped or plain) for a single sample,
@@ -120,10 +124,8 @@
 Output
 ------
 **Results CSV**
-    A comma-separated file summarising the relative abundance of each taxon
-    detected in the sample.  Columns include taxon name, taxonomic rank, number
-    of reads assigned, relative abundance (%), and the number of unique k-mers
-    supporting the assignment.
+    A comma-separated file with columns: taxid, reads, abundance, uniq.
+    Only taxa with non-zero relative abundance are reported.
 
     Example output for the "Plodia" test sample::
 
diff -r e6b5e7a0d7e7 -r dd206296acbf tool-data/mitokmer_probe_db.loc.sample
--- a/tool-data/mitokmer_probe_db.loc.sample	Fri Sep 11 22:01:39 2026 +0000
+++ b/tool-data/mitokmer_probe_db.loc.sample	Mon Sep 14 19:47:05 2026 +0000
@@ -1,18 +1,18 @@
 # mitoKmer Probe Database Location File
-# 
+#
 # This file lists the mitochondrial k-mer probe databases available to mitoKmer.
 # Entries are tab-separated; do NOT use spaces as delimiters.
 #
+# The database consists of a DIRECTORY containing multiple supporting .txt files
+# (e.g. mitochondria7_data.txt, mitochondria7_key.txt, refKeym7.txt, etc.)
+# The path column should point to that directory.
+#
 # Columns (tab-separated):
 #   value  - unique identifier used internally by Galaxy (no spaces)
 #   name   - human-readable label shown in the tool dropdown
-#   path   - absolute path to the gzipped probe file (mitoch_probes.txt.gz)
+#   path   - absolute path to the database DIRECTORY
 #
 # Example entry (remove the leading # to activate):
 #
-# mito_v1	Mitochondrial DB v1	/galaxy/tool-data/mitokmer/mitoch_probes_v1.txt.gz
+# mitochondria7	Mitochondrial DB v7	/galaxy/tool-data/mitokmer/mitochondria7
 #
-# Multiple databases can be listed, one per line:
-#
-# mito_insects_v1	Insect Mitochondrial DB v1	/galaxy/tool-data/mitokmer/mitoch_probes_insects_v1.txt.gz
-# mito_vertebrates_v1	Vertebrate Mitochondrial DB v1	/galaxy/tool-data/mitokmer/mitoch_probes_vertebrates_v1.txt.gz