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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Daniel Blankenberg
f92b25d2f5
Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles. Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes. Future Enhancement: Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
83 lines
3.6 KiB
XML
83 lines
3.6 KiB
XML
<tool id="Grep1" name="Select" version="1.0.1">
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<description>lines that match an expression</description>
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<command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
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<inputs>
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<param format="txt" name="input" type="data" label="Select lines from"/>
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<param name="invert" type="select" label="that">
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<option value="false">Matching</option>
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<option value="true">NOT Matching</option>
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</param>
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<param name="pattern" size="40" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
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<sanitizer>
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<valid initial="string.printable">
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<remove value="'"/>
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</valid>
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<mapping initial="none">
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<add source="'" target="__sq__"/>
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</mapping>
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</sanitizer>
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</param>
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</inputs>
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<outputs>
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<data format="input" name="out_file1" metadata_source="input"/>
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</outputs>
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<tests>
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<test>
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<param name="input" value="1.bed"/>
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<param name="invert" value="false"/>
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<param name="pattern" value="^chr[0-9]*"/>
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<output name="out_file1" file="fs-grep.dat"/>
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</test>
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</tests>
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<help>
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.. class:: infomark
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**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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-----
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**Syntax**
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The select tool searches the data for lines containing or not containing a match to the given pattern. Regular Expression is introduced in this tool. A Regular Expression is a pattern describing a certain amount of text.
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- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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- **\\A** matches the beginning of a string(but not an internal line).
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- **\\d** matches a digit, same as [0-9].
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- **\\D** matches a non-digit.
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- **\\s** matches a whitespace character.
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- **\\S** matches anything BUT a whitespace.
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- **\\t** matches a tab.
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- **\\w** matches an alphanumeric character.
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- **\\W** matches anything but an alphanumeric character.
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- **(** .. **)** groups a particular pattern.
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- **\\Z** matches the end of a string(but not a internal line).
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- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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- **{n}** The preceding item is matched exactly n times.
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- **{n,}** The preceding item is matched n or more times.
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- **{n,m}** The preceding item is matched at least n times but not more than m times.
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- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
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- **.** Matches any single character except a newline.
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- ***** The preceding item will be matched zero or more times.
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- **?** The preceding item is optional and matched at most once.
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- **+** The preceding item will be matched one or more times.
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- **^** has two meaning:
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- matches the beginning of a line or string.
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- indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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- **$** matches the end of a line or string.
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- **\|** Separates alternate possibilities.
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-----
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**Example**
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- **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file.
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- **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
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- **([^,][0-9]{1,3})(,[0-9]{3})\*** would match a large integer that is properly separated with commas such as 23,078,651.
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- **(abc)|(def)** would match either "abc" or "def".
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- **^\\W+#** would match any line that is a comment.
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</help>
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</tool>
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