Mercurial > repos > galaxytrakr > mitokmer

annotate mitokmer.xml @ 0:adc887a1a6de draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
author galaxytrakr
date Fri, 11 Sep 2026 21:58:43 +0000
parents
children e6b5e7a0d7e7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
1 <tool id="mitokmer" name="mitoKmer" version="2.0+galaxy0.1" python_template_version="3.5" profile="21.05">
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>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
4 <container type="docker">quay.io/galaxytrakr/mitokmer2:latest</container>
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[
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
8 ## ── kmerread expects files at specific relative paths ─────────────────
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
9 ## ./mitoch/mitoch_probes.txt.gz - probe database
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
10 ## ./jobs1/jobs1.txt - jobs file listing sample reads
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
11 ## It is invoked with no arguments: ./kmerread
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
12 mkdir -p ./mitoch ./jobs1 ./reads &&
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
13
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
14 ## ── Link probe database to the path kmerread expects ─────────────────
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
15 ln -sf '${probe_db.fields.path}' ./mitoch/mitoch_probes.txt.gz &&
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
16
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
17 ## ── Stage input reads ─────────────────────────────────────────────────
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
18 #for read in $reads
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
19 ln -sf '${read}' ./reads/${read.element_identifier.replace(' ', '_')} &&
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
20 #end for
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
21
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
22 ## ── Write the jobs file in the format kmerread expects ───────────────
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
23 ## Line 1: <sample_name> <number_of_files>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
24 ## Lines 2+: absolute path to each read file, one per line
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
25 #set sample_name = $reads[0].element_identifier.replace(' ', '_').split('_')[:-1] | join('_')
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
26 echo "${sample_name} ${reads|length}" > ./jobs1/jobs1.txt &&
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
27 #for read in $reads
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
28 echo "\$PWD/reads/${read.element_identifier.replace(' ', '_')}" >> ./jobs1/jobs1.txt &&
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
29 #end for
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
30
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
31 ## ── Run kmerread (reads jobs1/jobs1.txt and mitoch/mitoch_probes.txt.gz
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
32 ## by convention; no CLI arguments) ──────────────────────────────────
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
33 kmerread &&
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
34
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
35 ## ── Summarise results into CSV ────────────────────────────────────────
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
36 python3 /opt/mitokmer2/kmer_read_m7.py
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
37 -i ./jobs1
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
38 -o '${results_csv}'
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
39 ]]></command>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
40
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
41 <inputs>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
42 <!-- Probe database selected from Galaxy data table -->
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
43 <param name="probe_db"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
44 type="select"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
45 label="Mitochondrial k-mer probe database"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
46 help="Select a pre-installed mitochondrial k-mer probe database.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
47 Databases are managed by your Galaxy administrator via the
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
48 mitokmer_probe_db data table.">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
49 <options from_data_table="mitokmer_probe_db">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
50 <filter type="sort_by" column="1" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
51 <validator type="no_options"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
52 message="No mitochondrial k-mer probe databases are
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
53 currently installed. Please contact your
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
54 Galaxy administrator." />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
55 </options>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
56 </param>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
57
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
58 <!-- One or more FASTQ/FASTA files for a single sample -->
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
59 <param name="reads"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
60 type="data_collection"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
61 collection_type="list"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
62 format="fastq,fastq.gz,fasta,fasta.gz"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
63 label="Input reads (FASTQ or FASTA, gzipped or plain)"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
64 help="Provide one or more read files for a single sample as a Galaxy
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
65 list collection. Paired-end files (R1 + R2) should both be
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
66 included in the same collection. Light quality trimming of
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
67 read ends is performed internally; pre-trimming is optional." />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
68 </inputs>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
69
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
70 <outputs>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
71 <data name="results_csv"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
72 format="csv"
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
73 label="mitoKmer results for ${on_string}" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
74 </outputs>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
75
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
76 <tests>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
77 <test>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
78 <param name="probe_db" value="mitoch_probes_sample" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
79 <param name="reads">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
80 <collection type="list">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
81 <element name="Plodia_R1" value="test/Plodia_R1.fastq.gz" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
82 <element name="Plodia_R2" value="test/Plodia_R2.fastq.gz" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
83 </collection>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
84 </param>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
85 <output name="results_csv">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
86 <assert_contents>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
87 <has_text text="Plodia" />
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
88 </assert_contents>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
89 </output>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
90 </test>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
91 </tests>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
92
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
93 <help><![CDATA[
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
94 **mitoKmer** — Metagenomic Mitochondrial Read Identification by K-mer Database
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
95 ===============================================================================
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
96
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
97 Overview
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
98 --------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
99 mitoKmer identifies the taxonomic origin of short-read shotgun sequencing data
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
100 by matching reads against a database of species-specific mitochondrial k-mer
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
101 probes. It reports the relative abundance of taxa at multiple taxonomic ranks
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
102 (e.g. order, species) along with the number of matching reads and supporting
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
103 unique k-mers.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
104
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
105 Inputs
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
106 ------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
107 **Mitochondrial k-mer probe database**
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
108 Select a pre-installed probe database from the dropdown. Databases are
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
109 managed by your Galaxy administrator and registered in the
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
110 ``mitokmer_probe_db`` data table.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
111
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
112 **Input reads**
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
113 One or more FASTQ or FASTA files (gzipped or plain) for a single sample,
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
114 supplied as a Galaxy list collection. Both paired-end files (R1 and R2)
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
115 should be included in the same collection.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
116
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
117 * Pre-trimming is optional — the tool performs simple window-based quality
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
118 trimming of read ends internally.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
119
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
120 Output
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
121 ------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
122 **Results CSV**
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
123 A comma-separated file summarising the relative abundance of each taxon
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
124 detected in the sample. Columns include taxon name, taxonomic rank, number
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
125 of reads assigned, relative abundance (%), and the number of unique k-mers
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
126 supporting the assignment.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
127
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
128 Example output for the "Plodia" test sample::
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
129
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
130 Rank Taxon Reads Rel_Abund(%) Unique_kmers
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
131 Order Lepidoptera 10 0.1 329
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
132 Species Plodia interpunctella 462 99.9 466
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
133
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
134 Citation
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
135 --------
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
136 Please cite the mitoKmer GitHub repository if you use this tool in published work.
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
137 ]]></help>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
138
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
139 <citations>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
140 <citation type="bibtex">
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
141 @misc{githubmitokmer2,
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
142 author = {Mammel, Mark},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
143 title = {mitoKmer2},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
144 year = {2024},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
145 publisher = {GitHub},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
146 journal = {GitHub repository},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
147 url = {https://github.com/mmammel8/mitokmer2},
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
148 }
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
149 </citation>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
150 </citations>
adc887a1a6de planemo upload commit 927c4ee71df7d19ceb10446a04618af22c99d839
galaxytrakr
parents:
diff changeset
151 </tool>