Mercurial > repos > galaxytrakr > mitokmer

annotate mitokmer.xml @ 4:ecf96ad08611 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
author galaxytrakr
date Tue, 15 Sep 2026 12:02:36 +0000
parents dd206296acbf
children 8f4abeb27625
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.2" python_template_version="3.5" profile="21.05">
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
2 <description>Identify metagenomic mitochondrial reads by k-mer database matching</description>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
3 <requirements>
4
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
4 <container type="docker">quay.io/galaxytrakr/mitokmer:e57a559</container>
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
5 </requirements>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
6
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
8 ## ── All paths are hardcoded in kmer_read_m7.py: ──────────────────────
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
9 ## database: ./mitochondria7/<multiple .txt files>
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
10 ## jobs file: ./jobs7m/jobs7m.txt
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
11 ## output: ./jobs7m/jobs7m.csv
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
12 ## binary: ./kmerread7 (called as subprocess by the Python script)
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
13 mkdir -p ./mitochondria7 ./jobs7m &&
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
14
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
15 ## ── Link database files from the data table directory ─────────────────
4
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
16 ## Symlink each file individually from the registered database directory.
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
17 ## Note: glob must be outside quotes so the shell expands it correctly.
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
18 ln -sf '${probe_db.fields.path}'/* ./mitochondria7/ &&
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
19
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
20 ## ── Symlink kmerread7 into the working directory ──────────────────────
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
21 ## kmer_read_m7.py calls ./kmerread7 (relative path), so it must exist
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
22 ## in the Galaxy job working directory
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
23 ln -sf /usr/local/bin/kmerread7 ./kmerread7 &&
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
24
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
25 ## ── Write the jobs file ───────────────────────────────────────────────
4
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
26 ## Format: sample_name <tab> num_files
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
27 ## /abs/path/to/read1
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
28 ## /abs/path/to/read2 ...
4
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
29 ## Use len() to safely get collection size as an integer
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
30 #set sample_name = $reads.name.replace(' ', '_')
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
31 #set read_count = len($reads)
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
32 printf '%s\t%d\n' '${sample_name}' ${read_count} > ./jobs7m/jobs7m.txt &&
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
33 #for read in $reads
4
ecf96ad08611 planemo upload commit 26a6ad9e9ae7fdb967832a65f5173ea347da7f6c
galaxytrakr
parents: 2
diff changeset
34 printf '%s\n' '${read.file_name}' >> ./jobs7m/jobs7m.txt &&
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
35 #end for
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
36
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
37 ## ── Run the Python orchestrator (no arguments) ────────────────────────
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
38 ## kmer_read_m7.py reads jobs7m/jobs7m.txt, calls ./kmerread7,
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
39 ## and writes results to jobs7m/jobs7m.csv
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
40 python3 /opt/mitokmer2/kmer_read_m7.py &&
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
41
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
42 ## ── Copy output CSV to Galaxy output path ─────────────────────────────
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
43 cp ./jobs7m/jobs7m.csv '${results_csv}'
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
44 ]]></command>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
45
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
46 <inputs>
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
47 <!-- Probe database directory selected from Galaxy data table -->
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
48 <param name="probe_db"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
49 type="select"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
50 label="Mitochondrial k-mer probe database"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
51 help="Select a pre-installed mitochondrial k-mer probe database.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
52 Databases are managed by your Galaxy administrator via the
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
53 mitokmer_probe_db data table.">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
54 <options from_data_table="mitokmer_probe_db">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
55 <filter type="sort_by" column="1" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
56 <validator type="no_options"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
57 message="No mitochondrial k-mer probe databases are
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
58 currently installed. Please contact your
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
59 Galaxy administrator." />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
60 </options>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
61 </param>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
62
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
63 <param name="reads"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
64 type="data_collection"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
65 collection_type="list"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
66 format="fastq,fastq.gz,fasta,fasta.gz"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
67 label="Input reads (FASTQ or FASTA, gzipped or plain)"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
68 help="Provide one or more read files for a single sample as a Galaxy
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
69 list collection. Paired-end files (R1 + R2) should both be
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
70 included in the same collection. Light quality trimming of
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
71 read ends is performed internally; pre-trimming is optional." />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
72 </inputs>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
73
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
74 <outputs>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
75 <data name="results_csv"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
76 format="csv"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
77 label="mitoKmer results for ${on_string}" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
78 </outputs>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
79
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
80 <tests>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
81 <test>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
82 <param name="probe_db" value="mitoch_probes_sample" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
83 <param name="reads">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
84 <collection type="list">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
85 <element name="Plodia_R1" value="test/Plodia_R1.fastq.gz" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
86 <element name="Plodia_R2" value="test/Plodia_R2.fastq.gz" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
87 </collection>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
88 </param>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
89 <output name="results_csv">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
90 <assert_contents>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
91 <has_text text="Plodia" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
92 </assert_contents>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
93 </output>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
94 </test>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
95 </tests>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
96
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
97 <help><![CDATA[
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
98 **mitoKmer** — Metagenomic Mitochondrial Read Identification by K-mer Database
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
99 ===============================================================================
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
100
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
101 Overview
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
102 --------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
103 mitoKmer identifies the taxonomic origin of short-read shotgun sequencing data
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
104 by matching reads against a database of species-specific mitochondrial k-mer
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
105 probes. It reports the relative abundance of taxa at multiple taxonomic ranks
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
106 (e.g. order, species) along with the number of matching reads and supporting
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
107 unique k-mers.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
108
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
109 Inputs
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
110 ------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
111 **Mitochondrial k-mer probe database**
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
112 Select a pre-installed probe database from the dropdown. Databases are
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
113 managed by your Galaxy administrator and registered in the
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
114 ``mitokmer_probe_db`` data table. The database consists of a directory
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
115 of supporting ``.txt`` files.
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
116
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
117 **Input reads**
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
118 One or more FASTQ or FASTA files (gzipped or plain) for a single sample,
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
119 supplied as a Galaxy list collection. Both paired-end files (R1 and R2)
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
120 should be included in the same collection.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
121
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
122 * Pre-trimming is optional — the tool performs simple window-based quality
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
123 trimming of read ends internally.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
124
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
125 Output
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
126 ------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
127 **Results CSV**
2
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
128 A comma-separated file with columns: taxid, reads, abundance, uniq.
dd206296acbf planemo upload commit 83cba09882dc583100b39b69b41cf791e4efb55a
galaxytrakr
parents: 1
diff changeset
129 Only taxa with non-zero relative abundance are reported.
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
130
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
131 Example output for the "Plodia" test sample::
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
132
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
133 Rank Taxon Reads Rel_Abund(%) Unique_kmers
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
134 Order Lepidoptera 10 0.1 329
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
135 Species Plodia interpunctella 462 99.9 466
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
136
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
137 Citation
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
138 --------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
139 Please cite the mitoKmer GitHub repository if you use this tool in published work.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
140 ]]></help>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
141
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
142 <citations>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
143 <citation type="bibtex">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
144 @misc{githubmitokmer2,
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
145 author = {Mammel, Mark},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
146 title = {mitoKmer2},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
147 year = {2024},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
148 publisher = {GitHub},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
149 journal = {GitHub repository},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
150 url = {https://github.com/mmammel8/mitokmer2},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
151 }
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
152 </citation>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
153 </citations>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
154 </tool>