Mercurial > repos > iuc > windowmasker

annotate windowmasker_ustat.xml @ 0:d90ae4a02efd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
1 <tool id="windowmasker_ustat" name="WindowMasker ustat" version="1.0" profile="22.01">
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
2 <description>Mask sequences using a WindowMasker unit counts table</description>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
3 <macros>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
4 <import>macros.xml</import>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
5 </macros>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
6 <expand macro="requirements" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
7 <command detect_errors="exit_code">
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
8 <![CDATA[
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
9 windowmasker -ustat '${mkcount_input}'
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
10 -infmt fasta
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
11 -in '${fasta_input}'
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
12 -outfmt '${output_format}'
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
13 ${parse_seqids}
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
14
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
15 #if str($use_dust.use_dust_selector) == "yes":
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
16 -dust true
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
17 -dust_level ${use_dust.dust_level}
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
18 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
19
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
20 #if $adv.set_t_high:
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
21 -set_t_high $adv.set_t_high
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
22 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
23 #if $adv.set_t_high:
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
24 -set_t_low $adv.set_t_high
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
25 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
26 #if $adv.t_extend
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
27 -t_extend $adv.t_extend
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
28 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
29 #if $adv.t_low
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
30 -t_low $adv.t_low
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
31 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
32 #if $adv.t_high
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
33 -t_high $adv.t_high
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
34 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
35 #if $adv.t_thres
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
36 -t_thres $adv.t_thres
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
37 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
38 #if $adv.window
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
39 -window $adv.window
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
40 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
41
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
42 ## Convert WindowMasker interval output to BED format
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
43 #if str($output_format) == "interval":
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
44 | perl '${__tool_directory__}/windowmasker_to_bed.pl' > '${mask_output}'
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
45 #else
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
46 -out '${mask_output}'
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
47 #end if
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
48 ]]>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
49 </command>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
50 <inputs>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
51 <param argument="-in" name="fasta_input" type="data" format="fasta"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
52 label="FASTA sequence file" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
53
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
54 <param name="mkcount_input" type="data" format="txt"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
55 label="Unit counts produced by WindowMasker mkcount" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
56
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
57 <param argument="-parse_seqids" type="boolean" checked="false"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
58 truevalue="-parse_seqids" falsevalue=""
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
59 label="Parse Seq-ids in FASTA input" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
60
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
61 <conditional name="use_dust">
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
62 <param argument="-dust" name="use_dust_selector" type="select" label="Use DUST to mask low complexity sequences?" >
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
63 <option value="yes">Yes</option>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
64 <option value="no">No</option>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
65 </param>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
66 <when value="yes">
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
67 <param argument="-dust_level" type="integer" min="1" value="20" label="DUST level"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
68 help="Score threshold for subwindows" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
69 </when>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
70 <when value="no"></when>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
71 </conditional>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
72
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
73 <param name="output_format" type="select" label="Output format">
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
74 <option value="fasta">FASTA</option>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
75 <option value="interval" selected="true">BED</option>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
76 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
77 <option value="maskinfo_asn1_text">maskinfo ASN.1 text</option>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
78 <option value="maskinfo_xml">maskinfo XML</option>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
79 </param>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
80
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
81 <section name="adv" title="Advanced options" expanded="false">
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
82
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
83 <param argument="-set_t_high" type="integer" label="set_t_high"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
84 min="0" optional="true"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
85 help="Score for units with unit count greater than T_high" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
86
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
87 <param argument="-set_t_low" type="integer" label="set_t_low"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
88 min="0" optional="true"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
89 help="Score for units with unit count less than T_low" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
90
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
91 <param argument="-t_extend" type="integer" label="t_extend"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
92 min="0" optional="true"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
93 help="Override the t_extend value in the unit counts file" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
94
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
95 <param argument="-t_low" type="integer" label="t_low"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
96 min="0" optional="true"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
97 help="Override the t_low value in the unit counts file" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
98
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
99 <param argument="-t_high" type="integer" label="t_high"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
100 min="0" optional="true"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
101 help="Override the t_high value in the unit counts file" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
102
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
103 <param argument="-t_thres" type="integer" label="Score threshold"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
104 min="0" optional="true"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
105 help="Override the score threshold value in the unit counts file" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
106
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
107 <param argument="-window" type="integer" label="Size of the sliding window"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
108 min="0" optional="true"
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
109 help="The default is unit_size + 4" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
110 </section>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
111 </inputs>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
112 <outputs>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
113 <data name="mask_output" format="bed">
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
114 <change_format>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
115 <when input="output_format" value="fasta" format="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
116 <when input="output_format" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
117 <when input="output_format" value="maskinfo_asn1_text" format="maskinfo-asn1" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
118 <when input="output_format" value="maskinfo_xml" format="xml" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
119 </change_format>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
120 </data>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
121 </outputs>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
122 <tests>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
123 <test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
124 <!-- Test WindowMasker ustat with fasta output -->
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
125 <param name="fasta_input" value="contigs.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
126 <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
127 <param name="output_format" value="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
128 <output name="mask_output" file="contigs.wm.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
129 </test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
130 <test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
131 <!-- Test WindowMasker ustat with ASN.1 text output -->
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
132 <param name="fasta_input" value="contigs.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
133 <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
134 <param name="output_format" value="maskinfo_asn1_text" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
135 <output name="mask_output" file="contigs.wm.asn1" ftype="maskinfo-asn1"/>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
136 </test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
137 <test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
138 <!-- Test WindowMasker ustat with ASN.1 binary output -->
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
139 <param name="fasta_input" value="contigs.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
140 <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
141 <param name="output_format" value="maskinfo_asn1_bin" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
142 <output name="mask_output" file="contigs.wm.asnb" ftype="maskinfo-asn1-binary"/>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
143 </test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
144 <test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
145 <!-- Test WindowMasker ustat with XML output -->
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
146 <param name="fasta_input" value="contigs.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
147 <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
148 <param name="output_format" value="maskinfo_xml" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
149 <output name="mask_output" file="contigs.wm.xml" ftype="xml"/>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
150 </test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
151 <test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
152 <!-- Test WindowMasker ustat with advanced settings -->
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
153 <param name="fasta_input" value="contigs.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
154 <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
155 <param name="set_t_high" value="10" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
156 <param name="set_t_low" value="9" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
157 <param name="t_extend" value="5" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
158 <param name="t_low" value="9" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
159 <param name="t_high" value="10" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
160 <param name="t_thres" value="20" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
161 <param name="window" value="50" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
162 <output name="mask_output" file="contigs.advanced_wm.bed" ftype="bed"/>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
163 </test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
164 <test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
165 <!-- Test WindowMasker ustat without dust -->
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
166 <param name="fasta_input" value="contigs.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
167 <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
168 <param name="use_dust_selector" value="no" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
169 <output name="mask_output" file="contigs.nodust_wm.bed" ftype="bed"/>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
170 </test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
171 <test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
172 <!-- Test WindowMasker ustat with parse Seq-ids -->
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
173 <param name="fasta_input" value="contigs.fa" ftype="fasta" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
174 <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
175 <param name="parse_seqids" value="-parse_seqids" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
176 <output name="mask_output" file="contigs.seqid_wm.bed" ftype="bed"/>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
177 </test>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
178 </tests>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
179 <help>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
180 <![CDATA[
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
181 **What it does**
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
182
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
183 This tool runs `stage 2 <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/>`_
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
184 of the WindowMasker analysis to identify repeats within the input sequences.
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
185
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
186 .. class:: infomark
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
187
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
188 **Output formats:**
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
189
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
190 * Use the **binary or text maskinfo ASN.1** output formats to generate the mask file for
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
191 the `NCBI BLAST+ makeblastdb tool <https://www.ncbi.nlm.nih.gov/books/NBK279681/#_cookbook_Create_BLAST_database_with_the_>`_
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
192 * Use the BED output format to generate a list of masked regions
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
193
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
194
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
195 .. class:: infomark
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
196
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
197 **Advanced options:**
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
198
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
199 * See the `WindowMasker README file <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/README>`_
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
200 for additional details on the WindowMasker repeat masking options
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
201
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
202 ]]></help>
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
203 <expand macro="citations" />
d90ae4a02efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
iuc
parents:
diff changeset
204 </tool>