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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/kmerfinder commit 07d7ccc46c4387a3d9be4d99fa4671fc230cff1e-dirty"
author thanhlv
date Thu, 18 Nov 2021 18:00:28 +0000
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-1:000000000000 0:b868a5fd2653
1 <tool id="kmerfinder" name="Kmerfinder" version="@VERSION@+galaxy0">
2 <description> Species identification using kmer</description>
3 <macros>
4 <token name="@VERSION@">3.0.2</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">kmerfinder</requirement>
8 <!-- <container type="singularity">kmerfinder.sif</container> -->
9 </requirements>
10 <version_command>echo "3.0.2"</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 #import re
13 #if $input.is_of_type('fastqsanger', 'fastq'):
14 #set $ext = 'fastq'
15 #elif $input.is_of_type('fastqsanger.gz'):
16 #set $ext = 'fastq.gz'
17 #elif $input.is_of_type('fastq'):
18 #set $ext = 'fastq'
19 #elif $input.is_of_type('fastq.gz'):
20 #set $ext = 'fastq.gz'
21 #elif $input.is_of_type('fasta.gz'):
22 #set $ext = 'fasta.gz'
23 #elif $input.is_of_type('fasta'):
24 #set $ext = 'fasta'
25 #end if
26 #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
27 ln -fs '$input' $safename.$ext &&
28
29 kmerfinder.py
30 -i '$safename.$ext'
31 -db '${kmerfinder_databases.fields.path}.ATG'
32 -tax '${kmerfinder_databases.fields.path}.tax'
33 -o output
34 ]]> </command>
35 <inputs>
36 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" multiple="false" label="Sequence files" help="Fasta for Fastq"/>
37 <!-- DATABASE INPUT-->
38 <param label="Select a database" name="kmerfinder_databases" type="select">
39 <options from_data_table="kmerfinder_databases">
40 <validator message="No database is available" type="no_options" />
41 </options>
42 </param>
43 </inputs>
44 <outputs>
45 <data name="results" format="tabular" label="${tool.name} on ${on_string} Results" from_work_dir="output/results.txt"/>
46 </outputs>
47 <tests>
48 <test>
49 <param name="input" value="test.fastq.gz" ftype="fastqsanger.gz"/>
50 <param name="kmerfinder_databases" value="pseudomonas"/>
51 <output name="results">
52 <assert_contents>
53 <has_text text="Pseudomonas aeruginosa genome assembly PAO1OR" />
54 <has_text text="NZ_LN871187.1" />
55 </assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help><![CDATA[
60 Kmerfinder finds the best match (species identification) to the reads in one or more fastq files or one fasta file in a (kmer) database produced using the KMA program. The method outputs the best matches, along with additional taxonomic information, if that option is selected.
61
62 _`Document`: https://bitbucket.org/genomicepidemiology/kmerfinder
63
64 ]]></help>
65 <citations>
66 <citation type="doi">10.1128/JCM.02981-13</citation>
67 <citation type="doi">10.1128/JCM.02452-13</citation>
68 <citation type="doi">10.1186/s12859-018-2336-6</citation>
69 </citations>
70
71 </tool>