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comparison seqkit_locate.xml @ 4:5fb2dc40c4de draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 99c10c3df0424268179b3f54f89e01a34b9e120e
author iuc
date Sat, 18 May 2024 23:11:47 +0000
parents 6510652376b1
children
comparison
equal deleted inserted replaced
3:7e30613be1c6 4:5fb2dc40c4de
18 $conditional_pattern.use_regexp 18 $conditional_pattern.use_regexp
19 #else 19 #else
20 --pattern-file '$conditional_pattern.pattern_file' 20 --pattern-file '$conditional_pattern.pattern_file'
21 #end if 21 #end if
22 $output_mode 22 $output_mode
23 --validate-seq-length $advanced_options.validate_seq_length
24 $advanced_options.circular 23 $advanced_options.circular
25 $advanced_options.degenerate 24 $advanced_options.degenerate
26 $advanced_options.hide_matched 25 $advanced_options.hide_matched
27 $advanced_options.ignore_case 26 $advanced_options.ignore_case
28 #if not $advanced_options.degenerate 27 #if not $advanced_options.degenerate
37 > '$output' 36 > '$output'
38 ]]></command> 37 ]]></command>
39 <inputs> 38 <inputs>
40 <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/> 39 <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>
41 <conditional name="conditional_pattern"> 40 <conditional name="conditional_pattern">
42 <param name="mode" type="select" label="Pattern mode" 41 <param name="mode" type="select" label="Pattern mode" help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
43 help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular
44 expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
45 <option value="expression">Pattern/motif sequence</option> 42 <option value="expression">Pattern/motif sequence</option>
46 <option value="file">FASTA file with the pattern/motif of interest</option> 43 <option value="file">FASTA file with the pattern/motif of interest</option>
47 </param> 44 </param>
48 <when value="expression"> 45 <when value="expression">
49 <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed"> 46 <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">
50 <sanitizer invalid_char=""> 47 <sanitizer invalid_char="">
51 <valid initial="string.letters,string.digits"> 48 <valid initial="string.letters,string.digits">
52 <add value="^"/> 49 <add value="^"/>
53 <add value="$"/> 50 <add value="$"/>
54 <add value="("/> 51 <add value="("/>
55 <add value=")"/> 52 <add value=")"/>
56 <add value="|"/> 53 <add value="|"/>
57 <add value="?"/> 54 <add value="?"/>
58 <add value="*"/> 55 <add value="*"/>
59 <add value="+"/> 56 <add value="+"/>
60 <add value="{"/> 57 <add value="{"/>
61 <add value="}"/> 58 <add value="}"/>
62 <add value="\"/> 59 <add value="\"/>
63 <add value="["/> 60 <add value="["/>
64 <add value="]"/> 61 <add value="]"/>
65 <add value="."/> 62 <add value="."/>
66 <add value=","/> 63 <add value=","/>
67 </valid> 64 </valid>
68 </sanitizer> 65 </sanitizer>
69 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator> 66 <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
70 </param> 67 </param>
71 <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/> 68 <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>
84 <option value="">Tabular (default format)</option> 81 <option value="">Tabular (default format)</option>
85 <option value="--gtf">GTF</option> 82 <option value="--gtf">GTF</option>
86 <option value="--bed">BED6</option> 83 <option value="--bed">BED6</option>
87 </param> 84 </param>
88 <section name="advanced_options" title="Advanced options"> 85 <section name="advanced_options" title="Advanced options">
89 <param argument="--validate-seq-length" type="integer" min="0" value="10000" label="Lenth of the sequence to validate" help="Default: 10000" /> 86 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" checked="false" label="Circular genome" help="When using flag --circular, end position of matched subsequence that crossing genome sequence end would be greater than sequence length"/>
90 <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" checked="false" label="Circular genome" 87 <param argument="--degenerate" type="boolean" truevalue="--degenerate" falsevalue="" checked="false" label="Pattern/motif contains degenerate bases" help="Do not use degenerate bases/residues in regular expression, you need convert them to regular expression, e.g., change 'N' or 'X' to '.'"/>
91 help="When using flag --circular, end position of matched subsequence that crossing genome sequence end would be greater than sequence length" />
92 <param argument="--degenerate" type="boolean" truevalue="--degenerate" falsevalue="" checked="false" label="Pattern/motif contains degenerate bases"
93 help="Do not use degenerate bases/residues in regular expression, you need convert them to regular expression, e.g., change 'N' or 'X' to '.'"/>
94 <param argument="--hide-matched" type="boolean" truevalue="--hide-matched" falsevalue="" checked="false" label="Do not show matched sequences"/> 88 <param argument="--hide-matched" type="boolean" truevalue="--hide-matched" falsevalue="" checked="false" label="Do not show matched sequences"/>
95 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" checked="false" label="Ignore case"/> 89 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" checked="false" label="Ignore case"/>
96 <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="--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"/>
97 <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="--non-greedy" type="boolean" truevalue="--non-greedy" falsevalue="" checked="false" label="Non-greedy mode" help="Faster, but muy miss motifs overlapping with others"/>
98 <param argument="--only-positive-strand" type="boolean" truevalue="--only-positive-strand" falsevalue="" checked="false" label="Only search on positive strand"/> 92 <param argument="--only-positive-strand" type="boolean" truevalue="--only-positive-strand" falsevalue="" checked="false" label="Only search on positive strand"/>
99 <param argument="--use-fmi" type="boolean" truevalue="--use-fmi" falsevalue="" checked="false" label="FM-index" 93 <param argument="--use-fmi" type="boolean" truevalue="--use-fmi" falsevalue="" checked="false" label="FM-index" help="Use FM-index for much faster search of lots of sequence patterns. This option is not compatible with the --degenerate option"/>
100 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: &gt;gi|110645304|ref|NC_002516.2| Pseud..."/>
101 <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..." />
102 </section> 95 </section>
103 </inputs> 96 </inputs>
104 <outputs> 97 <outputs>
105 <data name="output" format="tabular" label="${tool.name} on ${on_string}"> 98 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
106 <change_format> 99 <change_format>
191 5. When using flag --circular, end position of matched subsequence that 184 5. When using flag --circular, end position of matched subsequence that
192 crossing genome sequence end would be greater than sequence length. 185 crossing genome sequence end would be greater than sequence length.
193 </help> 186 </help>
194 <expand macro="citations"/> 187 <expand macro="citations"/>
195 </tool> 188 </tool>
196