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comparison mitokmer.xml @ 4:ecf96ad08611 draft

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planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
author galaxytrakr
date Tue, 15 Sep 2026 12:02:36 +0000
parents dd206296acbf
children 8f4abeb27625
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3:45ac0b1424fc 4:ecf96ad08611
1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.1" python_template_version="3.5" profile="21.05"> 1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.2" python_template_version="3.5" profile="21.05">
2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description> 2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description>
3 <requirements> 3 <requirements>
4 <container type="docker">quay.io/galaxytrakr/mitokmer:927c4ee</container> 4 <container type="docker">quay.io/galaxytrakr/mitokmer:e57a559</container>
5 </requirements> 5 </requirements>
6 6
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ## ── All paths are hardcoded in kmer_read_m7.py: ────────────────────── 8 ## ── All paths are hardcoded in kmer_read_m7.py: ──────────────────────
9 ## database: ./mitochondria7/<multiple .txt files> 9 ## database: ./mitochondria7/<multiple .txt files>
11 ## output: ./jobs7m/jobs7m.csv 11 ## output: ./jobs7m/jobs7m.csv
12 ## binary: ./kmerread7 (called as subprocess by the Python script) 12 ## binary: ./kmerread7 (called as subprocess by the Python script)
13 mkdir -p ./mitochondria7 ./jobs7m && 13 mkdir -p ./mitochondria7 ./jobs7m &&
14 14
15 ## ── Link database files from the data table directory ───────────────── 15 ## ── Link database files from the data table directory ─────────────────
16 ## The data table path points to a directory containing all the 16 ## Symlink each file individually from the registered database directory.
17 ## mitochondria7 .txt files; symlink each one into ./mitochondria7/ 17 ## Note: glob must be outside quotes so the shell expands it correctly.
18 ln -sf '${probe_db.fields.path}'/* ./mitochondria7/ && 18 ln -sf '${probe_db.fields.path}'/* ./mitochondria7/ &&
19 19
20 ## ── Symlink kmerread7 into the working directory ────────────────────── 20 ## ── Symlink kmerread7 into the working directory ──────────────────────
21 ## kmer_read_m7.py calls ./kmerread7 (relative path), so it must exist 21 ## kmer_read_m7.py calls ./kmerread7 (relative path), so it must exist
22 ## in the Galaxy job working directory 22 ## in the Galaxy job working directory
23 ln -sf /usr/local/bin/kmerread7 ./kmerread7 && 23 ln -sf /usr/local/bin/kmerread7 ./kmerread7 &&
24 24
25 ## ── Write the jobs file ─────────────────────────────────────────────── 25 ## ── Write the jobs file ───────────────────────────────────────────────
26 ## Format: sample_name num_files 26 ## Format: sample_name <tab> num_files
27 ## /abs/path/to/read1 27 ## /abs/path/to/read1
28 ## /abs/path/to/read2 ... 28 ## /abs/path/to/read2 ...
29 #set sample_name = $reads[0].element_identifier.replace(' ', '_').split('_')[:-1] | join('_') 29 ## Use len() to safely get collection size as an integer
30 printf '${sample_name}\t${reads|length}\n' > ./jobs7m/jobs7m.txt && 30 #set sample_name = $reads.name.replace(' ', '_')
31 #set read_count = len($reads)
32 printf '%s\t%d\n' '${sample_name}' ${read_count} > ./jobs7m/jobs7m.txt &&
31 #for read in $reads 33 #for read in $reads
32 printf '${read.file_name}\n' >> ./jobs7m/jobs7m.txt && 34 printf '%s\n' '${read.file_name}' >> ./jobs7m/jobs7m.txt &&
33 #end for 35 #end for
34 36
35 ## ── Run the Python orchestrator (no arguments) ──────────────────────── 37 ## ── Run the Python orchestrator (no arguments) ────────────────────────
36 ## kmer_read_m7.py reads jobs7m/jobs7m.txt, calls ./kmerread7, 38 ## kmer_read_m7.py reads jobs7m/jobs7m.txt, calls ./kmerread7,
37 ## and writes results to jobs7m/jobs7m.csv 39 ## and writes results to jobs7m/jobs7m.csv
56 currently installed. Please contact your 58 currently installed. Please contact your
57 Galaxy administrator." /> 59 Galaxy administrator." />
58 </options> 60 </options>
59 </param> 61 </param>
60 62
61 <!-- One or more FASTQ/FASTA files for a single sample -->
62 <param name="reads" 63 <param name="reads"
63 type="data_collection" 64 type="data_collection"
64 collection_type="list" 65 collection_type="list"
65 format="fastq,fastq.gz,fasta,fasta.gz" 66 format="fastq,fastq.gz,fasta,fasta.gz"
66 label="Input reads (FASTQ or FASTA, gzipped or plain)" 67 label="Input reads (FASTQ or FASTA, gzipped or plain)"