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comparison windowmasker_mkcounts.xml @ 0:d90ae4a02efd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
author iuc
date Thu, 14 Dec 2023 16:04:27 +0000
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1 <tool id="windowmasker_mkcounts" name="WindowMasker mkcounts" version="1.0" profile="22.01">
2 <description>Construct WindowMasker unit counts table</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 windowmasker -mk_counts -infmt fasta
10 #if $adv.genome_size
11 -genome_size $adv.genome_size
12 #end if
13 #if $adv.t_low
14 -t_low $adv.t_low
15 #end if
16 #if $adv.t_high
17 -t_high $adv.t_high
18 #end if
19 #if $adv.unit
20 -unit $adv.unit
21 #end if
22
23 -sformat ${adv.sformat}
24 ${adv.checkdup}
25 -in '${fasta_input}'
26 -out '${mkcount_output}'
27 ]]>
28 </command>
29 <inputs>
30 <param argument="-in" name="fasta_input" type="data" format="fasta"
31 label="FASTA sequence file" />
32
33 <section name="adv" title="Advanced options" expanded="false" >
34 <param argument="-checkdup" type="boolean" checked="false"
35 truevalue="-checkdup" falsevalue=""
36 label="Check input file for potentially duplicated sequences" />
37
38 <param argument="-genome_size" type="integer" label="Genome size"
39 min="0" optional="true"
40 help="Use this genome size to compute the unit length" />
41
42 <param argument="-sformat" type="select" label="Unit counts format"
43 help="The format the unit counts data should be generated" >
44 <option value="ascii">Plain text (ascii)</option>
45 <option value="oascii" selected="true">Optimized text (oascii)</option>
46 <!-- Omit support for non-portable binary formats (binary, obinary) -->
47 </param>
48
49 <param argument="-t_low" type="integer" label="T_low"
50 min="0" optional="true"
51 help="Save only units that appears at least this many times" />
52
53 <param argument="-t_high" type="integer" label="T_high"
54 min="0" optional="true"
55 help="Set the maximum count value for units" />
56
57 <param argument="-unit" type="integer" label="Unit length"
58 min="1" max="16" optional="true"
59 help="Unit length used to mask the genome" />
60 </section>
61 </inputs>
62 <outputs>
63 <data name="mkcount_output" format="txt" />
64 </outputs>
65 <tests>
66 <test>
67 <!-- Test mkcounts with default settings -->
68 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
69 <output name="mkcount_output" file="chr4_part.oascii.counts" />
70 </test>
71 <test>
72 <!-- Test mkcounts with custom genome_size -->
73 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
74 <param name="genome_size" value="500000" />
75 <output name="mkcount_output" file="chr4_part.500k_size.counts" />
76 </test>
77 <test>
78 <!-- Test mkcounts with ascii output format -->
79 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
80 <param name="sformat" value="ascii" />
81 <output name="mkcount_output" file="chr4_part.ascii.counts" />
82 </test>
83 <test>
84 <!-- Test mkcounts with custom unit settings -->
85 <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
86 <param name="t_low" value="3" />
87 <param name="t_high" value="20" />
88 <param name="unit" value="9" />
89 <output name="mkcount_output" file="chr4_part.custom_unit.counts" />
90 </test>
91 </tests>
92 <help>
93 <![CDATA[
94 **What it does**
95
96 This tool runs `stage 1 <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/>`_
97 of the WindowMasker analysis to produce a unit counts file for a genome assembly.
98
99 ]]></help>
100 <expand macro="citations" />
101 </tool>