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comparison seqkit_locate.xml @ 0:642d73815dd1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
author iuc
date Thu, 03 Nov 2022 19:35:37 +0000
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children 6510652376b1
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1 <tool id="seqkit_locate" name="SeqKit locate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>subsequences/motifs, mismatch allowed</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10
11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
12 ln -s '${input}' '${input_identifier}' &&
13
14 seqkit locate
15 --threads \${GALAXY_SLOTS:-4}
16 #if $conditional_pattern.mode == 'expression'
17 --pattern '"$conditional_pattern.pattern"'
18 $conditional_pattern.use_regexp
19 #else
20 --pattern-file '$conditional_pattern.pattern_file'
21 #end if
22 $output_mode
23 --validate-seq-length $advanced_options.validate_seq_length
24 $advanced_options.circular
25 $advanced_options.degenerate
26 $advanced_options.hide_matched
27 $advanced_options.ignore_case
28 #if not $advanced_options.degenerate
29 --max-mismatch $advanced_options.max_mismatch
30 $advanced_options.use_fmi
31 #end if
32 $advanced_options.non_greedy
33 $advanced_options.only_positive_strand
34 $advanced_options.id_ncbi
35 '${input_identifier}'
36 > '$output'
37 ]]></command>
38 <inputs>
39 <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>
40 <conditional name="conditional_pattern">
41 <param name="mode" type="select" label="Pattern mode"
42 help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular
43 expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
44 <option value="expression">Pattern/motif sequence</option>
45 <option value="file">FASTA file with the pattern/motif of interest</option>
46 </param>
47 <when value="expression">
48 <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">
49 <sanitizer invalid_char="">
50 <valid initial="string.letters,string.digits">
51 <add value="^"/>
52 <add value="$"/>
53 <add value="("/>
54 <add value=")"/>
55 <add value="|"/>
56 <add value="?"/>
57 <add value="*"/>
58 <add value="+"/>
59 <add value="{"/>
60 <add value="}"/>
61 <add value="\"/>
62 <add value="["/>
63 <add value="]"/>
64 <add value="."/>
65 <add value=","/>
66 </valid>
67 </sanitizer>
68 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
69 </param>
70 <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>
71 </when>
72 <when value="file">
73 <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>
74 </when>
75 </conditional>
76 <param name="output_mode" type="select" label="Output mode">
77 <option value="">Tabular (default format)</option>
78 <option value="--gtf">GTF</option>
79 <option value="--bed">BED6</option>
80 </param>
81 <section name="advanced_options" title="Advanced options">
82 <param argument="--validate-seq-length" type="integer" min="0" value="10000" label="Lenth of the sequence to validate" help="Default: 10000" />
83 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" checked="false" label="Circular genome"
84 help="When using flag --circular, end position of matched subsequence that crossing genome sequence end would be greater than sequence length" />
85 <param argument="--degenerate" type="boolean" truevalue="--degenerate" falsevalue="" checked="false" label="Pattern/motif contains degenerate bases"
86 help="Do not use degenerate bases/residues in regular expression, you need convert them to regular expression, e.g., change 'N' or 'X' to '.'"/>
87 <param argument="--hide-matched" type="boolean" truevalue="--hide-matched" falsevalue="" checked="false" label="Do not show matched sequences"/>
88 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" checked="false" label="Ignore case"/>
89 <param argument="--max-mismatch" type="integer" min="0" value="0" label="Maximum mismatch" help="For large genomes like human genome, using mapping/alignment tools would be faster" />
90 <param argument="--non-greedy" type="boolean" truevalue="--non-greedy" falsevalue="" checked="false" label="Non-greedy mode" help="Faster, but muy miss motifs overlapping with others" />
91 <param argument="--only-positive-strand" type="boolean" truevalue="--only-positive-strand" falsevalue="" checked="false" label="Only search on positive strand"/>
92 <param argument="--use-fmi" type="boolean" truevalue="--use-fmi" falsevalue="" checked="false" label="FM-index"
93 help="Use FM-index for much faster search of lots of sequence patterns. This option is not compatible with the --degenerate option"/>
94 <param argument="--id-ncbi" type="boolean" truevalue="--id-ncbi" falsevalue="" checked="false" label="FASTA head is NCBI stype" help="Example: >gi|110645304|ref|NC_002516.2| Pseud..." />
95 </section>
96 </inputs>
97 <outputs>
98 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
99 <change_format>
100 <when input="output_mode" value="--gtf" format="gtf"/>
101 <when input="output_mode" value="--bed" format="bed"/>
102 </change_format>
103 </data>
104 </outputs>
105 <tests>
106 <test expect_num_outputs="1">
107 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
108 <conditional name="conditional_pattern">
109 <param name="mode" value="expression"/>
110 <param name="pattern" value="ATAGAT"/>
111 </conditional>
112 <section name="advanced_options">
113 <param name="max_mismatch" value="1"/>
114 </section>
115 <output name="output" file="locate_output1.tabular" ftype="tabular"/>
116 </test>
117 <test expect_num_outputs="1">
118 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
119 <conditional name="conditional_pattern">
120 <param name="mode" value="expression"/>
121 <param name="pattern" value="A[TU]G"/>
122 <param name="use_regexp" value="true"/>
123 </conditional>
124 <param name="output_mode" value="--bed"/>
125 <section name="advanced_options">
126 <param name="circular" value="true"/>
127 <param name="hide_matched" value="true"/>
128 <param name="ignore_case" value="true"/>
129 <param name="only_positive_strand" value="true"/>
130 <param name="id_ncbi" value="true"/>
131 </section>
132 <output name="output" file="locate_output2.bed" ftype="bed"/>
133 </test>
134 <test expect_num_outputs="1">
135 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
136 <conditional name="conditional_pattern">
137 <param name="mode" value="file"/>
138 <param name="pattern_file" value="motif_sequence.fasta"/>
139 </conditional>
140 <param name="output_mode" value="--gtf"/>
141 <section name="advanced_options">
142 <param name="use_fmi" value="true"/>
143 </section>
144 <output name="output" file="locate_output3.gtf" ftype="gtf"/>
145 </test>
146 </tests>
147 <help>
148 .. class:: infomark
149
150 **Purpose**
151
152 Locate subsequences/motifs, mismatch allowed.
153
154 ------
155
156 .. class:: infomark
157
158 **Attention**
159
160 1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
161 expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
162 2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
163 But do not use degenerate bases/residues in regular expression, you need
164 convert them to regular expression, e.g., change "N" or "X" to ".".
165 3. When providing search patterns (motifs) via flag '-p',
166 please use double quotation marks for patterns containing comma,
167 e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
168 parser accepts comma-separated-values (CSV) for multiple values (motifs).
169 Patterns in file do not follow this rule.
170 4. Mismatch is allowed using flag "-m/--max-mismatch",
171 you can increase the value of "-j/--threads" to accelerate processing.
172 5. When using flag --circular, end position of matched subsequence that
173 crossing genome sequence end would be greater than sequence length.
174 </help>
175 <expand macro="citations"/>
176 </tool>
177