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1 <tool id="cshl_grep_tool" name="grep" version="0.1.1">
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2 <description></description>
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3 <command interpreter="sh">grep_wrapper.sh '$input1' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive</command>
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4 <inputs>
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5 <param format="txt" name="input1" type="data" label="Select lines from" />
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6
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7 <param name="invert" type="select" label="that">
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8 <option value="">Match</option>
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9 <option value="-v">Don't Match</option>
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10 </param>
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11
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12 <param name="url_paste" type="text" size="40" label="Regular Expression" help="See below for more details">
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13 <sanitizer>
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14 <valid initial="string.printable">
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15 <remove value="'"/>
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16 </valid>
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17 </sanitizer>
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18 </param>
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19
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20 <param name="case_sensitive" type="select" label="Match type">
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21 <option value="-i">case insensitive</option>
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22 <option value="">case sensitive</option>
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23 </param>
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24
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25 <param name="lines_before" type="integer" label="Show lines preceding the matched line (-B)" help="leave it at zero unless you know what you're doing" value="0" />
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26 <param name="lines_after" type="integer" label="Show lines trailing the matched line (-A)" help="leave it at zero unless you know what you're doing" value="0" />
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27
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28 <param name="color" type="select" label="Output">
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29 <option value="NOCOLOR">text file (for further processing)</option>
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30 <option value="COLOR">Highlighted HTML (for easier viewing)</option>
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31 </param>
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32
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33 </inputs>
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34 <outputs>
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35 <data format="input" name="output" metadata_source="input1"
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36 >
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37 <change_format>
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38 <when input="color" value="COLOR" format="html"
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39 />
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40 </change_format>
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41 </data>
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42 </outputs>
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43 <help>
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44
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45 **What it does**
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46
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47 This tool runs the unix **grep** command on the selected data file.
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48
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49 .. class:: infomark
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50
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51 **TIP:** This tool uses the **perl** regular expression syntax (same as running 'grep -P'). This is **NOT** the POSIX or POSIX-extended syntax (unlike the awk/sed tools).
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52
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53
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54 **Further reading**
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55
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56 - Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
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57 - Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf)
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58 - Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)
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59
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60 -----
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61
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62 **Grep Examples**
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63
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64 - **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**)
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65 - **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC
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66 - **TTT.{4,10}AAA** would match lines with 3 Ts, followed by 4 to 10 characters (any characeters), followed by 3 As.
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67 - **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file.
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68 - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
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69 - **hsa|mmu** would match lines containing "hsa" or "mmu" (or both).
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70
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71 -----
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72
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73 **Regular Expression Syntax**
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74
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75 The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.
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76
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77 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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78 - **^** matches the beginning of a string(but not an internal line).
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79 - **\\d** matches a digit, same as [0-9].
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80 - **\\D** matches a non-digit.
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81 - **\\s** matches a whitespace character.
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82 - **\\S** matches anything BUT a whitespace.
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83 - **\\t** matches a tab.
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84 - **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
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85 - **\\W** matches anything but an alphanumeric character.
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86 - **(** .. **)** groups a particular pattern.
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87 - **\\Z** matches the end of a string(but not a internal line).
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88 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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89
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90 - **{n}** The preceding item is matched exactly n times.
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91 - **{n,}** The preceding item ismatched n or more times.
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92 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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93
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94 - **[** ... **]** 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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95 - **.** Matches any single character except a newline.
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96 - ***** The preceding item will be matched zero or more times.
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97 - **?** The preceding item is optional and matched at most once.
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98 - **+** The preceding item will be matched one or more times.
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99 - **^** has two meaning:
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100 - matches the beginning of a line or string.
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101 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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102 - **$** matches the end of a line or string.
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103 - **\|** Separates alternate possibilities.
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104
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105
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106 </help>
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107 </tool>
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