Mercurial > repos > iuc > seqkit_locate
changeset 4:5fb2dc40c4de draft default tip
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 | 7e30613be1c6 |
| children | |
| files | macros.xml seqkit_locate.xml test-data/stats_output1.tabular test-data/stats_output2.tabular |
| diffstat | 4 files changed, 28 insertions(+), 36 deletions(-) [+] |
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--- a/macros.xml Fri Mar 29 09:46:41 2024 +0000 +++ b/macros.xml Sat May 18 23:11:47 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.3.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.8.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.09</token> <xml name="bio_tools"> <xrefs>
--- a/seqkit_locate.xml Fri Mar 29 09:46:41 2024 +0000 +++ b/seqkit_locate.xml Sat May 18 23:11:47 2024 +0000 @@ -20,7 +20,6 @@ --pattern-file '$conditional_pattern.pattern_file' #end if $output_mode ---validate-seq-length $advanced_options.validate_seq_length $advanced_options.circular $advanced_options.degenerate $advanced_options.hide_matched @@ -39,9 +38,7 @@ <inputs> <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/> <conditional name="conditional_pattern"> - <param name="mode" type="select" label="Pattern mode" - help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular - expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs"> + <param name="mode" type="select" label="Pattern mode" help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs"> <option value="expression">Pattern/motif sequence</option> <option value="file">FASTA file with the pattern/motif of interest</option> </param> @@ -49,21 +46,21 @@ <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> - <add value="^"/> - <add value="$"/> - <add value="("/> - <add value=")"/> - <add value="|"/> - <add value="?"/> - <add value="*"/> - <add value="+"/> - <add value="{"/> - <add value="}"/> - <add value="\"/> - <add value="["/> - <add value="]"/> - <add value="."/> - <add value=","/> + <add value="^"/> + <add value="$"/> + <add value="("/> + <add value=")"/> + <add value="|"/> + <add value="?"/> + <add value="*"/> + <add value="+"/> + <add value="{"/> + <add value="}"/> + <add value="\"/> + <add value="["/> + <add value="]"/> + <add value="."/> + <add value=","/> </valid> </sanitizer> <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator> @@ -86,19 +83,15 @@ <option value="--bed">BED6</option> </param> <section name="advanced_options" title="Advanced options"> - <param argument="--validate-seq-length" type="integer" min="0" value="10000" label="Lenth of the sequence to validate" help="Default: 10000" /> - <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" /> - <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 '.'"/> + <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"/> + <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 '.'"/> <param argument="--hide-matched" type="boolean" truevalue="--hide-matched" falsevalue="" checked="false" label="Do not show matched sequences"/> <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" checked="false" label="Ignore case"/> - <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" /> - <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" /> + <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"/> + <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"/> <param argument="--only-positive-strand" type="boolean" truevalue="--only-positive-strand" falsevalue="" checked="false" label="Only search on positive strand"/> - <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"/> - <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..." /> + <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"/> + <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..."/> </section> </inputs> <outputs> @@ -193,4 +186,3 @@ </help> <expand macro="citations"/> </tool> -
--- a/test-data/stats_output1.tabular Fri Mar 29 09:46:41 2024 +0000 +++ b/test-data/stats_output1.tabular Sat May 18 23:11:47 2024 +0000 @@ -1,2 +1,2 @@ -file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%) GC(%) -input1_fastq_gz FASTQ DNA 5 505 101 101.0 101 50.5 101.0 50.5 0 101 98.02 89.31 35.45 +file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%) +input1_fastq_gz FASTQ DNA 5 505 101 101.0 101 101.0 101.0 101.0 0 101 1 98.02 89.31 25.93 35.45
--- a/test-data/stats_output2.tabular Fri Mar 29 09:46:41 2024 +0000 +++ b/test-data/stats_output2.tabular Sat May 18 23:11:47 2024 +0000 @@ -1,2 +1,2 @@ -file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 Q20(%) Q30(%) GC(%) -input1_fasta_gz FASTA DNA 3 10732 1213 3577.3 4796 2968.0 4723.0 4759.5 0 4723 0.00 0.00 48.15 +file format type num_seqs sum_len min_len avg_len max_len Q1 Q2 Q3 sum_gap N50 N50_num Q20(%) Q30(%) AvgQual GC(%) +input1_fasta_gz FASTA DNA 3 10732 1213 3577.3 4796 2968.0 4723.0 4759.5 0 4723 2 0.00 0.00 0.00 48.15