Mercurial > repos > galaxy-australia > kmc
comparison kmc.xml @ 0:ca2743037241 draft default tip
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
author | galaxy-australia |
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date | Tue, 27 Sep 2022 05:20:06 +0000 |
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-1:000000000000 | 0:ca2743037241 |
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1 <tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > | |
2 <description>K-mer counting and filtering of reads</description> | |
3 <xrefs> | |
4 <xref type='bio.tools'>kmc</xref> | |
5 </xrefs> | |
6 <macros> | |
7 <import>macros.xml</import> | |
8 </macros> | |
9 <expand macro="requirements" /> | |
10 <expand macro="stdio" /> | |
11 <expand macro="version_command" /> | |
12 <command><![CDATA[ | |
13 kmc | |
14 -t\${GALAXY_SLOTS:-4} | |
15 #if $params.k: | |
16 -k'$params.k' | |
17 #end if | |
18 #if $params.m: | |
19 -m'$params.m' | |
20 #end if | |
21 #if $params.j: | |
22 -j'$statistic' | |
23 #end if | |
24 #if $params.exclude_length: | |
25 -ci'$params.exclude_length' | |
26 #end if | |
27 #if $params.max_counter_value: | |
28 -cs'$params.max_counter_value' | |
29 #end if | |
30 #if $input_file.is_of_type("fastq"): | |
31 -fq | |
32 #elif $input_file.is_of_type("fasta"): | |
33 -fm | |
34 #elif $input_file.is_of_type("bam"): | |
35 -fbam | |
36 #elif $input_file.is_of_type("kmc_suf"): | |
37 -fkmc | |
38 #end if | |
39 $input_file | |
40 db | |
41 . | |
42 | |
43 ]]></command> | |
44 <inputs> | |
45 <expand macro="macro_input" /> | |
46 <section name="params" title="parameter" expanded="false"> | |
47 <param argument="-k" type="integer" value="25" label="k-mer length (k from 1 to 256; default: 25)" /> | |
48 <param argument="-m" type="integer" value="12" label="max amount of RAM in GB (from 1 to 1024); default: 12" /> | |
49 <param name="signature_length" arguments="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/> | |
50 <param name="exclude_length" arguments="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/> | |
51 <param name="max_counter_value" arguments="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/> | |
52 <param name="exclude_kmer_occurence" arguments="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/> | |
53 <param argument="-j" type="boolean" truevalue="-j" falsevalue="" checked="True" label="file name with execution summary in JSON format"/> | |
54 </section> | |
55 </inputs> | |
56 <outputs> | |
57 <data format="json" name="statistic" label="${tool.name} on ${on_string}"> | |
58 <filter>params['j']</filter> | |
59 </data> | |
60 <collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db"> | |
61 <data format="binary" name="db.kmc_suf" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_suf" /> | |
62 <data format="binary" name="db.kmc_pre" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_pre" /> | |
63 </collection> | |
64 </outputs> | |
65 | |
66 <tests> | |
67 <test> | |
68 <!-- #1 test fastq with common parameters --> | |
69 <param name="input_file" value="F3D0_R1.fastq" ftype="fastq"/> | |
70 <param name="k" value="25" /> | |
71 <param name="m" value="12" /> | |
72 <param name="p" value="9" /> | |
73 <param name="ci" value="2" /> | |
74 <param name="cs" value="255" /> | |
75 <output name="db.kmc_suf" file="db.kmc_suf" ftype="binary" /> | |
76 <output name="db.kmc_pre" file="db.kmc_pre" ftype="binary" /> | |
77 </test> | |
78 <test> | |
79 <!-- #2 test fasta with common parameters --> | |
80 <param name="input_file" value="contigs.fa" ftype="fasta"/> | |
81 <param name="k" value="27" /> | |
82 <param name="m" value="24" /> | |
83 <param name="ci" value="2" /> | |
84 <param name="cs" value="255" /> | |
85 <param name="fm" value="-fm" /> | |
86 <output name="contig_kmer27.kmc_suf" file="contig_kmer27.kmc_suf" ftype="binary" /> | |
87 <output name="contig_kmer27.kmc_pre" file="contig_kmer27.kmc_pre" ftype="binary" /> | |
88 </test> | |
89 </tests> | |
90 <help><![CDATA[ | |
91 | |
92 .. class:: infomark | |
93 | |
94 **What it does** | |
95 | |
96 *K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.* | |
97 | |
98 | |
99 **Input** | |
100 | |
101 - input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ. | |
102 | |
103 **Example:** | |
104 | |
105 - kmc -k27 -m24 NA19238.fastq NA.res /data/kmc_tmp_dir/ | |
106 - kmc -k27 -m24 @files.lst NA.res /data/kmc_tmp_dir/ | |
107 | |
108 **Output** | |
109 | |
110 - filename.res.kmc_suf | |
111 - filename.res.kmc_pre | |
112 | |
113 | |
114 .. class:: infomark | |
115 | |
116 **References** | |
117 | |
118 More information are available on `website <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_. | |
119 ]]></help> | |
120 <citations> | |
121 <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation> | |
122 <citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation> | |
123 <citation type="doi">DOI: 10.1186/1471-2105-14-160</citation> | |
124 </citations> | |
125 </tool> |