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comparison windowmasker_ustat.xml @ 0:f80c9e6700ba draft default tip

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