Mercurial > repos > yating-l > windowmasker_2_5_0
comparison windowmasker_mkcounts.xml @ 0:f80c9e6700ba draft default tip
planemo upload commit 91a780909d1eda07d17f6aebf7f08f0c024b6a25
author | yating-l |
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date | Tue, 16 May 2017 13:18:12 -0400 |
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-1:000000000000 | 0:f80c9e6700ba |
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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> |