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planemo upload commit 91a780909d1eda07d17f6aebf7f08f0c024b6a25
author yating-l
date Tue, 16 May 2017 13:18:12 -0400
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1 <?xml version="1.0"?>
2 <tool id="windowmasker_mkcounts" name="WindowMasker_mkcounts" version="1.0">
3 <description>Construct WindowMasker unit counts table</description>
4
5 <macros>
6 <import>windowmasker_macros.xml</import>
7 </macros>
8
9 <expand macro="requirements" />
10
11 <command detect_errors="exit_code">
12 <![CDATA[
13 @OPTIONAL_PARAM_FUNC@
14
15 windowmasker -mk_counts -infmt fasta
16
17 $optional_param("-genome_size", $adv.genome_size)
18 $optional_param("-t_low", $adv.t_low)
19 $optional_param("-t_high", $adv.t_high)
20 $optional_param("-unit", $adv.unit)
21
22 -sformat ${adv.sformat} -checkdup ${adv.checkdup}
23 -in "${fasta_input}" -out "${mkcount_output}"
24 ]]>
25 </command>
26 <inputs>
27 <param name="fasta_input" type="data" format="fasta"
28 label="FASTA sequence file" />
29
30 <section name="adv" title="Advanced options" expanded="false" >
31 <param name="checkdup" type="boolean" checked="false"
32 truevalue="true" falsevalue="false"
33 label="Check input file for potentially duplicated sequences"
34 help="-checkdup" />
35
36 <param name="genome_size" type="integer" label="Genome size"
37 min="0" optional="true"
38 help="Use this genome size to compute the unit length" />
39
40 <param name="sformat" type="select" label="Unit counts format"
41 help="The format the unit counts data should be generated" >
42
43 <option value="ascii">Plain text (ascii)</option>
44 <option value="oascii" selected="true">Optimized text (oascii)</option>
45 <!-- Omit support for non-portable binary formats (binary, obinary) -->
46 </param>
47
48 <param name="t_low" type="integer" label="T_low"
49 min="0" optional="true"
50 help="Save only units that appears at least this many times" />
51
52 <param name="t_high" type="integer" label="T_high"
53 min="0" optional="true"
54 help="Set the maximum count value for units" />
55
56 <param name="unit" type="integer" label="Unit length"
57 min="1" max="16" optional="true"
58 help="Unit length used to mask the genome" />
59 </section>
60 </inputs>
61 <outputs>
62 <data name="mkcount_output" format="txt" />
63 </outputs>
64 <tests>
65 <test>
66 <!-- Test mkcounts with default settings -->
67 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
68 <output name="mkcount_output" file="chr4_part.oascii.counts" />
69 </test>
70 <test>
71 <!-- Test mkcounts with custom genome_size -->
72 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
73 <param name="genome_size" value="500000" />
74 <output name="mkcount_output" file="chr4_part.500k_size.counts" />
75 </test>
76 <test>
77 <!-- Test mkcounts with ascii output format -->
78 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
79 <param name="sformat" value="ascii" />
80 <output name="mkcount_output" file="chr4_part.ascii.counts" />
81 </test>
82 <test>
83 <!-- Test mkcounts with custom unit settings -->
84 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
85 <param name="t_low" value="3" />
86 <param name="t_high" value="20" />
87 <param name="unit" value="9" />
88 <output name="mkcount_output" file="chr4_part.custom_unit.counts" />
89 </test>
90 </tests>
91 <help>
92 <![CDATA[
93 **What it does**
94
95 This tool runs `stage 1 <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/>`_
96 of the WindowMasker analysis to produce a unit counts file for a genome assembly.
97
98 ]]></help>
99
100 <expand macro="citations" />
101 </tool>