Mercurial > repos > galaxy-australia > kmc
comparison kmc_tools_filter.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_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > | |
2 <description>filtering KMC's database</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 #for $f in $input_collection: | |
14 #if '.kmc_suf' in str($f.element_identifier) | |
15 ln -s '${f}' db.kmc_suf && | |
16 #else | |
17 ln -s '${f}' db.kmc_pre && | |
18 #end if | |
19 #end for | |
20 kmc_tools | |
21 filter | |
22 -t\${GALAXY_SLOTS:-2} | |
23 #if $t: | |
24 '$t' | |
25 #end if | |
26 #if $hm: | |
27 '$hm' | |
28 #end if | |
29 db | |
30 -ci'$min_kmer_occurrence' | |
31 -cx'$max_kmer_occurrence' | |
32 $input_read_file | |
33 -f'$input_format' | |
34 -ci'$exclude_length' | |
35 -cx'$exclude_kmer_occurence' | |
36 #if str($output_format) == 'q': | |
37 $filter_output_fastq | |
38 #else | |
39 $filter_output_fasta | |
40 #end if | |
41 -f'$output_format' | |
42 | |
43 ]]></command> | |
44 <inputs> | |
45 <param name="input_collection" type="data_collection" collection_type="list" label="KMC db"/> | |
46 <param name="input_read_file" type="data" format="fastq,fasta" label="input read file" help="Input file format FASTQ/FASTA [default:FASTQ]"/> | |
47 <expand macro="input_option"/> | |
48 <param name="input_format" argument="-f" type="select" label="input read file format [default:FASTQ]"> | |
49 <option value="q" selected="true">FASTQ</option> | |
50 <option value="a">FASTA</option> | |
51 </param> | |
52 <param argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="trim reads" help="trim reads on first invalid k-mer instead of remove entirely"/> | |
53 <param argument="-hm" type="boolean" truevalue="-hm" falsevalue="" checked="false" label="hard mask" help="hard mask invalid k-mers in a read"/> | |
54 <expand macro="general_option"/> | |
55 <param name="output_format" argument="-f" type="select" label="output read file format [default:FASTQ]"> | |
56 <option value="q" selected="true">FASTQ</option> | |
57 <option value="a">FASTA</option> | |
58 </param> | |
59 </inputs> | |
60 <outputs> | |
61 <data name="filter_output_fastq" format="fastq" label="${tool.name} on ${on_string}: filter"> | |
62 <filter>'q' in output_format</filter> | |
63 </data> | |
64 <data name="filter_output_fasta" format="fasta" label="${tool.name} on ${on_string}: filter"> | |
65 <filter>'a' in output_format</filter> | |
66 </data> | |
67 | |
68 </outputs> | |
69 | |
70 <tests> | |
71 <test> | |
72 <!-- #1 test with common parameters --> | |
73 <param name="input_collection"> | |
74 <collection type="list"> | |
75 <element name="db.kmc_suf" value="db.kmc_suf" dbkey="89"/> | |
76 <element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/> | |
77 </collection> | |
78 </param> | |
79 <param name="input_read_file" value="F3D0_R1.fastq" ftype="fastq"/> | |
80 <param name="min_kmer_occurrence" value="3" /> | |
81 <param name="exclude_length" value="2" /> | |
82 <param name="exclude_kmer_occurence" value="10" /> | |
83 <output name="filtered_1.fastq" file="filtered_1.fastq" ftype="fastq" /> | |
84 </test> | |
85 <test> | |
86 <!-- #2 test with common parameters --> | |
87 <param name="input_collection"> | |
88 <collection type="list"> | |
89 <element name="db.kmc_suf" value="db.kmc_suf" dbkey="89"/> | |
90 <element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/> | |
91 </collection> | |
92 </param> | |
93 <param name="input_read_file" value="F3D0_R1.fastq" ftype="fastq"/> | |
94 <param name="exclude_length" value="10" /> | |
95 <param name="exclude_kmer_occurence" value="100" /> | |
96 <output name="filtered_2.fastq" file="filtered_2.fastq" ftype="fastq" /> | |
97 </test> | |
98 | |
99 </tests> | |
100 <help><![CDATA[ | |
101 | |
102 .. class:: infomark | |
103 | |
104 **What it does** | |
105 | |
106 *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.* | |
107 | |
108 **Input** | |
109 | |
110 - input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ. | |
111 | |
112 **Command line Example:** | |
113 | |
114 - kmc_tools filter kmc_db -ci3 input.fastq -ci0.5 -cx1.0 filtered_1.fastq | |
115 - kmc_tools filter kmc_db input.fastq -ci10 -cx100 filtered_2.fastq | |
116 | |
117 **Output** | |
118 | |
119 - filtered_1.fastq | |
120 - filtered_2.fastq | |
121 | |
122 | |
123 .. class:: infomark | |
124 | |
125 **References** | |
126 | |
127 More information are available on `website <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_. | |
128 ]]></help> | |
129 <citations> | |
130 <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation> | |
131 <citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation> | |
132 <citation type="doi">DOI: 10.1186/1471-2105-14-160</citation> | |
133 </citations> | |
134 </tool> |