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1 <tool id="Grep1" name="Select" version="1.0.1">
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2 <description>lines that match an expression</description>
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3 <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
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4 <inputs>
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5 <param format="txt" name="input" type="data" label="Select lines from"/>
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6 <param name="invert" type="select" label="that">
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7 <option value="false">Matching</option>
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8 <option value="true">NOT Matching</option>
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9 </param>
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10 <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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11 <sanitizer>
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12 <valid initial="string.printable">
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13 <remove value="'"/>
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14 </valid>
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15 <mapping initial="none">
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16 <add source="'" target="__sq__"/>
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17 </mapping>
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18 </sanitizer>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data format="input" name="out_file1" metadata_source="input"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="1.bed"/>
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27 <param name="invert" value="false"/>
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28 <param name="pattern" value="^chr[0-9]*"/>
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29 <output name="out_file1" file="fs-grep.dat"/>
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30 </test>
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31 </tests>
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32 <help>
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33
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34 .. class:: infomark
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35
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36 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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37
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38 -----
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39
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40 **Syntax**
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41
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42 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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43
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44 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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45 - **\\A** matches the beginning of a string(but not an internal line).
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46 - **\\d** matches a digit, same as [0-9].
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47 - **\\D** matches a non-digit.
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48 - **\\s** matches a whitespace character.
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49 - **\\S** matches anything BUT a whitespace.
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50 - **\\t** matches a tab.
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51 - **\\w** matches an alphanumeric character.
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52 - **\\W** matches anything but an alphanumeric character.
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53 - **(** .. **)** groups a particular pattern.
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54 - **\\Z** matches the end of a string(but not a internal line).
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55 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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56
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57 - **{n}** The preceding item is matched exactly n times.
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58 - **{n,}** The preceding item is matched n or more times.
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59 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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60
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61 - **[** ... **]** 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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62 - **.** Matches any single character except a newline.
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63 - ***** The preceding item will be matched zero or more times.
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64 - **?** The preceding item is optional and matched at most once.
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65 - **+** The preceding item will be matched one or more times.
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66 - **^** has two meaning:
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67 - matches the beginning of a line or string.
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68 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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69 - **$** matches the end of a line or string.
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70 - **\|** Separates alternate possibilities.
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71
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72 -----
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73
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74 **Example**
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75
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76 - **^chr([0-9A-Za-z])+** would match lines that begin with chromosomes, such as lines in a BED format file.
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77 - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
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78 - **([^,][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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79 - **(abc)|(def)** would match either "abc" or "def".
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80 - **^\\W+#** would match any line that is a comment.
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81 </help>
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82 </tool>
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