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comparison mdust.xml @ 0:cc6db1ee2d48 draft

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author urgi-team
date Mon, 05 Oct 2015 11:05:21 -0400
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1 <?xml version="1.0"?>
2 <tool id="mdust" name="mdust" version="1.0">
3 <description>fast and symmetric DUST implementation to mask low-complexity DNA sequences</description>
4 <requirements>
5 <requirement type="package" version="1.0">mdust</requirement>
6 </requirements>
7 <command interpreter="python">
8 mdust_wrapper.py -i ${input_file} -v ${cutoff} -w ${wsize} -m ${masking_letter.masking_letter_selector} -f ${output_type.output_type_selector}
9
10 #if str( $output_type.output_type_selector) == "default"
11 -o ${output_masked_fasta}
12 #end if
13
14 #if str( $output_type.output_type_selector) == "tab"
15 -o ${output_tab}
16 #end if
17
18 #if str( $output_type.output_type_selector) == "bed"
19 -o ${output_bed}
20 #end if
21 </command>
22 <inputs>
23 <param name="input_file" type="data" format="fasta" label="Input fasta file" help=""/>
24 <param name="cutoff" type="integer" value="28" label="cutt-off" help="cut-off" />
25 <param name="wsize" type="integer" value="3" label="set maximum word size" help="word-size" />
26 <conditional name="masking_letter">
27 <param name="masking_letter_selector" type="select" label="Choose your masking type" help="Select the masking letter (N,X or lowercase)" >
28 <option value="N" selected="True">N (default)</option>
29 <option value="X">X</option>
30 <option value="L">lowercase</option>
31 </param>
32 </conditional>
33 <conditional name="output_type">
34 <param name="output_type_selector" type="select" label="Choose your output type" help="select your output">
35 <option value="default" selected="True">masked file (default)</option>
36 <option value="tab">output masking coordinates only (tab delimited)</option>
37 <option value="bed">output masking coordinates only (bed format)</option>
38 </param>
39 </conditional>
40 </inputs>
41 <outputs>
42 <data format="fasta" name="output_masked_fasta" label="masked.${input_file.name}">
43 <filter>( output_type['output_type_selector'] == 'default' )</filter>
44 </data>
45 <data format="tabular" name="output_tab" label="${input_file.name}.tab">
46 <filter>( output_type['output_type_selector'] == 'tab' )</filter>
47 </data>
48 <data format="bed" name="output_bed" label="${input_file.name}.bed">
49 <filter>( output_type['output_type_selector'] == 'bed' )</filter>
50 </data>
51 </outputs>
52 <tests>
53 <test>
54 <param name="input_file" value="seq-mdust.fsa" />
55 <output name="output_masked_fasta" file="masked-seq-mdust.fsa" ftype="fasta" />
56 </test>
57 </tests>
58 <help><![CDATA[
59 mdust new implementation of the DUST module that uses the same function to assign a complexity score to a sequence, but uses a different rule by which high-scoring sequences are masked.
60
61 -----
62
63 **Usage:** ::
64
65 mdust [<fasta-file>] [-w <wsize>] [-v <cut-off>] [-m N|X|L] [-c]
66 if no <fasta-file> is given, a multi-fasta stream is expected at stdin
67 -v default <cut-off> value is 28 (lower values might mask more,
68 but possibly still useful sequence; > 64 will rarely mask poly-triplets)
69 -w set maximum word size to <wsize> (default 3)
70 -m if fasta output is not disabled by -c, set the masking letter type:
71 N ('N', default), X ('X'), L (make lowercase)
72 -c output masking coordinates only:
73 seq_name, seqlength, mask_start, mask_end (tab delimited)
74
75 -----
76
77 **Reference:** ::
78
79 A fast and symmetric DUST implementation to mask low-complexity DNA sequences.
80 Morgulis A, Gertz EM, Schäffer AA, Agarwala R.
81 J Comput Biol. 2006 Jun;13(5):1028-40.
82 PMID:16796549
83
84
85 ]]>
86 </help>
87 </tool>