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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit d0b3d69f25fe8419e5b98165ae53b59651d711b1
author iuc
date Fri, 10 Oct 2025 12:03:10 +0000
parents 889cc43b72d6
children
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2:2c532a6eee3f 3:b221a6c2ed00
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01"> 2 <tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.6.6+galaxy0" profile="24.1">
3 <description>kma index builder</description> 3 <description>kma index builder</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.2.21">kma</requirement> 5 <requirement type="package" version="1.6.6">kma</requirement>
6 <requirement type="package" version="3.7">python</requirement>
7 </requirements> 6 </requirements>
8 <version_command>kma -v</version_command> 7 <version_command>kma -v</version_command>
9 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
10 <![CDATA[ 9 <![CDATA[
11 python '${__tool_directory__}/kma_build_index.py' 10 mkdir -p '${out_file.extra_files_path}'/index_folder &&
12 '${out_file}' 11 kma_index
13 --k ${k} 12 -i '$fasta'
14 --k_t ${k_t} 13 -o '${out_file.extra_files_path}'/index_folder/index
15 --k_i ${k_i} 14 ## index options
16 --ML ${ML} 15 -k $k
17 --ht ${ht} 16 -k_t $k_t
18 --hq ${hq} 17 -k_i $k_i
19 --name '${name}' 18 -ML $ML
20 '${fasta}' 19 -ht $ht
21 ]]> 20 -hq $hq
22 </command> 21 ]]></command>
22 <configfiles>
23 <configfile filename="dm.json"><![CDATA[#slurp
24 #from datetime import datetime
25 #from hashlib import md5
26 #set value=datetime.now().strftime("%Y-%m-%d") + "_" + md5($name.encode()).hexdigest()
27 {"data_tables": {"kma_index": [{"value": "$value", "name": "$name", "path": "index_folder"}]}}
28 ]]></configfile>
29 </configfiles>
23 <inputs> 30 <inputs>
24 <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." /> 31 <param argument="-k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
25 <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." /> 32 <param argument="-k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
26 <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." /> 33 <param argument="-k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
27 <param name="ML" type="integer" value="16" label="Minimum length of templates" /> 34 <param argument="-ML" type="integer" value="16" label="Minimum length of templates" />
28 <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" /> 35 <param argument="-ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
29 <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" /> 36 <param argument="-hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
30 <param name="name" type="text" label="Name for index" /> 37 <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
31 <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" /> 38 <param name="name" type="text" optional="false" label="Name for index" help="Choose a name that describes the indexed sequence and possibly any non-default indexing parameters.">
39 <validator type="empty_field"/>
40 </param>
32 </inputs> 41 </inputs>
33 <outputs> 42 <outputs>
34 <data name="out_file" format="data_manager_json" /> 43 <data name="out_file" format="data_manager_json" from_work_dir="dm.json"/>
35 </outputs> 44 </outputs>
36 <tests> 45 <tests>
37 <test> 46 <test>
38 <param name="fasta" value="phiX174.fasta"/> 47 <param name="fasta" value="phiX174.fasta"/>
39 <param name="name" value="index"/> 48 <param name="name" value="index"/>
40 <output name="out_file" value="kma_data_manager.json" compare="sim_size" /> 49 <output name="out_file" ftype="data_manager_json">
50 <assert_contents>
51 <has_text text='"kma_index":' />
52 <has_text text='"name": "index"' />
53 <has_text text='"path": "index_folder"' />
54 <has_text_matching expression='"value": "\d{4}-\d{2}-\d{2}_6a992d5529f459a44fee58c733255e86"' />
55 </assert_contents>
56 </output>
41 </test> 57 </test>
42 </tests> 58 </tests>
43 <help> 59 <help><![CDATA[
44 </help> 60 **Data manager for building an index for the kma aligner**
61
62 Runs the kma index command on the input sequence with the chosen options.
63
64 .. class:: infomark
65
66 You may want to capture details about the reference sequence and any non-default indexing parameters in the name of the index so that users have a better idea what they are selecting for tool runs.
67 ]]></help>
45 <citations> 68 <citations>
46 <citation type="doi">10.1186/s12859-018-2336-6</citation> 69 <citation type="doi">10.1186/s12859-018-2336-6</citation>
47 </citations> 70 </citations>
48 </tool> 71 </tool>