[3] | 1 | <tool id="cshl_grep_tool" name="grep"> |
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| 2 | <description></description> |
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| 3 | <command interpreter="sh">grep_wrapper.sh $input $output '$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="input" 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 | <!-- Note: the parameter ane MUST BE 'url_paste' - |
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| 13 | This is a hack in the galaxy library (see ./lib/galaxy/util/__init__.py line 142) |
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| 14 | If the name is 'url_paste' the string won't be sanitized, and all the non-alphanumeric characters |
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| 15 | will be passed to the shell script --> |
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| 16 | <param name="url_paste" type="text" size="40" label="Regular Expression" help=""> |
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| 17 | <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> |
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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" help="(same as grep -B, 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" help="(same as grep -A, 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 | <tests> |
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| 35 | <test> |
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| 36 | <!-- grep a FASTA file for sequences with specific motif --> |
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| 37 | <param name="input" value="unix_grep_input1.txt" /> |
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| 38 | <output name="output" file="unix_grep_output1.txt" /> |
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| 39 | <param name="case_sensitive" value="case sensitive" /> |
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| 40 | <param name="invert" value="" /> |
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| 41 | <param name="url_paste" value="AA.{2}GT" /> |
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| 42 | <param name="lines_before" value="1" /> |
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| 43 | <param name="lines_after" value="0" /> |
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| 44 | <param name="color" value="NOCOLOR" /> |
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| 45 | </test> |
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| 46 | <test> |
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| 47 | <!-- grep a FASTA file for sequences with specific motif - |
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| 48 | show highlighed output --> |
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| 49 | <param name="input" value="unix_grep_input1.txt" /> |
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| 50 | <output name="output" file="unix_grep_output2.html" /> |
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| 51 | <param name="case_sensitive" value="case sensitive" /> |
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| 52 | <param name="invert" value="" /> |
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| 53 | <param name="url_paste" value="AA.{2}GT" /> |
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| 54 | <param name="lines_before" value="0" /> |
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| 55 | <param name="lines_after" value="0" /> |
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| 56 | <param name="color" value="COLOR" /> |
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| 57 | </test> |
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| 58 | </tests> |
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| 59 | <outputs> |
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| 60 | <data format="input" name="output" metadata_source="input" > |
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| 61 | <change_format> |
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| 62 | <when input="color" value="COLOR" format="HTML" /> |
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| 63 | </change_format> |
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| 64 | </data> |
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| 65 | </outputs> |
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| 66 | <help> |
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| 67 | |
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| 68 | **What it does** |
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| 69 | |
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| 70 | This tool runs the unix **grep** command on the selected data file. |
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| 71 | |
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| 72 | .. class:: infomark |
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| 73 | |
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| 74 | **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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| 75 | |
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| 76 | |
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| 77 | **Further reading** |
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| 78 | |
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| 79 | - Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression) |
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| 80 | - Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf) |
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| 81 | - Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html) |
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| 82 | |
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| 83 | ----- |
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| 84 | |
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| 85 | **Grep Examples** |
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| 86 | |
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| 87 | - **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**) |
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| 88 | - **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC |
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| 89 | - **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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| 90 | - **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file. |
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| 91 | - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively. |
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| 92 | - **hsa|mmu** would match lines containing "hsa" or "mmu" (or both). |
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| 93 | |
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| 94 | ----- |
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| 95 | |
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| 96 | **Regular Expression Syntax** |
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| 97 | |
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| 98 | 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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| 99 | |
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| 100 | - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for. |
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| 101 | - **^** matches the beginning of a string(but not an internal line). |
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| 102 | - **\\d** matches a digit, same as [0-9]. |
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| 103 | - **\\D** matches a non-digit. |
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| 104 | - **\\s** matches a whitespace character. |
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| 105 | - **\\S** matches anything BUT a whitespace. |
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| 106 | - **\\t** matches a tab. |
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| 107 | - **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore ) |
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| 108 | - **\\W** matches anything but an alphanumeric character. |
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| 109 | - **(** .. **)** groups a particular pattern. |
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| 110 | - **\\Z** matches the end of a string(but not a internal line). |
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| 111 | - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern. |
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| 112 | |
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| 113 | - **{n}** The preceding item is matched exactly n times. |
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| 114 | - **{n,}** The preceding item ismatched n or more times. |
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| 115 | - **{n,m}** The preceding item is matched at least n times but not more than m times. |
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| 116 | |
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| 117 | - **[** ... **]** 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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| 118 | - **.** Matches any single character except a newline. |
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| 119 | - ***** The preceding item will be matched zero or more times. |
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| 120 | - **?** The preceding item is optional and matched at most once. |
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| 121 | - **+** The preceding item will be matched one or more times. |
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| 122 | - **^** has two meaning: |
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| 123 | - matches the beginning of a line or string. |
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| 124 | - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets. |
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| 125 | - **$** matches the end of a line or string. |
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| 126 | - **\|** Separates alternate possibilities. |
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| 127 | |
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| 128 | |
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| 129 | </help> |
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| 130 | </tool> |
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