Mercurial > repos > iuc > seqkit_locate
comparison seqkit_locate.xml @ 4:5fb2dc40c4de draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 99c10c3df0424268179b3f54f89e01a34b9e120e
author | iuc |
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date | Sat, 18 May 2024 23:11:47 +0000 |
parents | 6510652376b1 |
children |
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3:7e30613be1c6 | 4:5fb2dc40c4de |
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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: >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 |