comparison seqkit_locate.xml @ 2:03b29dff91e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 3dbd70c33e5adb451abd1cbd195c2e244c2b0c59

1:592e41e46dad

    $conditional_pattern.use_regexp
#else
    --pattern-file '$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
$advanced_options.ignore_case
#if not $advanced_options.degenerate

> '$output'
]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>
        <conditional name="conditional_pattern">
            <param name="mode" type="select" label="Pattern mode" 
                help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular
                    expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
                <option value="expression">Pattern/motif sequence</option>
                <option value="file">FASTA file with the pattern/motif of interest</option>
            </param>
            <when value="expression">
                <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">
                    <sanitizer invalid_char="">
                        <valid initial="string.letters,string.digits">
                        <add value="^"/>
                        <add value="$"/>
                        <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=","/>
                        </valid>
                    </sanitizer>
                    <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
                </param>
                <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>

            <option value="">Tabular (default format)</option>
            <option value="--gtf">GTF</option>
            <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="--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="--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..." />
        </section>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
            <change_format>

  5. When using flag --circular, end position of matched subsequence that 
     crossing genome sequence end would be greater than sequence length.
    </help>
    <expand macro="citations"/>
</tool>

2:03b29dff91e4

    $conditional_pattern.use_regexp
#else
    --pattern-file '$conditional_pattern.pattern_file'
#end if
$output_mode
$advanced_options.circular
$advanced_options.degenerate
$advanced_options.hide_matched
$advanced_options.ignore_case
#if not $advanced_options.degenerate

> '$output'
]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>
        <conditional name="conditional_pattern">
            <param name="mode" type="select" label="Pattern mode" help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular                     expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
                <option value="expression">Pattern/motif sequence</option>
                <option value="file">FASTA file with the pattern/motif of interest</option>
            </param>
            <when value="expression">
                <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">
                    <sanitizer invalid_char="">
                        <valid initial="string.letters,string.digits">
                            <add value="^"/>
                            <add value="$"/>
                            <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=","/>
                        </valid>
                    </sanitizer>
                    <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
                </param>
                <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>

            <option value="">Tabular (default format)</option>
            <option value="--gtf">GTF</option>
            <option value="--bed">BED6</option>
        </param>
        <section name="advanced_options" title="Advanced options">
            <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="--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: &gt;gi|110645304|ref|NC_002516.2| Pseud..."/>
        </section>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
            <change_format>

  5. When using flag --circular, end position of matched subsequence that 
     crossing genome sequence end would be greater than sequence length.
    </help>
    <expand macro="citations"/>
</tool>