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1 <tool id="unixtools_grep_tool" name="Search in textfiles" version="0.1.1">
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2 <description>(grep)</description>
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3 <requirements>
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4 <requirement type="package" version="8.21">gnu_coreutils</requirement>
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5 <requirement type="package" version="2.14">gnu_grep</requirement>
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6 <requirement type="set_environment">UNIX_TOOLS_SCRIPT_PATH</requirement>
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7 </requirements>
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8 <command interpreter="sh">
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9 #if $color = "COLOR":
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10 GREP_COLOR='1;34' grep --color=always -P "$@" -- "${url_paste}" '${input}' | \$UNIX_TOOLS_SCRIPT_PATH/ansi2html.sh > "${output}"
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11 #else:
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12 grep -P "$@" -- "${url_paste}" '${input}' | grep -v "^--$" > "${output}"
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13 #end if
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14
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15 ##grep_wrapper.sh '$input' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive
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16 </command>
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17 <inputs>
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18 <param format="txt" name="input" type="data" label="Select lines from" />
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19
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20 <param name="invert" type="select" label="that">
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21 <option value="">Match</option>
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22 <option value="-v">Don't Match</option>
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23 </param>
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24
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25 <param name="url_paste" type="text" size="40" label="Regular Expression" help="See below for more details">
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26 <sanitizer>
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27 <valid initial="string.printable">
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28 <remove value="'"/>
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29 </valid>
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30 </sanitizer>
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31 </param>
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32
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33 <param name="case_sensitive" type="select" label="Match type">
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34 <option value="-i">case insensitive</option>
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35 <option value="">case sensitive</option>
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36 </param>
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37
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38 <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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39 <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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40
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41 <param name="color" type="select" label="Output">
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42 <option value="NOCOLOR">text file (for further processing)</option>
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43 <option value="COLOR">Highlighted HTML (for easier viewing)</option>
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44 </param>
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45
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46 </inputs>
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47 <outputs>
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48 <data format="input" name="output" metadata_source="input">
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49 <change_format>
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50 <when input="color" value="COLOR" format="html"
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51 />
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52 </change_format>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <!-- grep a FASTA file for sequences with specific motif -->
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58 <param name="input" value="unix_grep_input1.txt" />
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59 <output name="output" file="unix_grep_output1.txt" />
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60 <param name="case_sensitive" value="case sensitive" />
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61 <param name="invert" value="" />
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62 <param name="url_paste" value="AA.{2}GT" />
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63 <param name="lines_before" value="1" />
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64 <param name="lines_after" value="0" />
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65 <param name="color" value="NOCOLOR" />
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66 </test>
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67 <test>
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68 <!-- grep a FASTA file for sequences with specific motif -
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69 show highlighed output -->
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70 <param name="input" value="unix_grep_input1.txt" />
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71 <output name="output" file="unix_grep_output2.html" />
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72 <param name="case_sensitive" value="case sensitive" />
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73 <param name="invert" value="" />
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74 <param name="url_paste" value="AA.{2}GT" />
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75 <param name="lines_before" value="0" />
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76 <param name="lines_after" value="0" />
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77 <param name="color" value="COLOR" />
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78 </test>
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79 </tests>
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80 <help>
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81
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82 **What it does**
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83
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84 This tool runs the unix **grep** command on the selected data file.
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85
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86 .. class:: infomark
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87
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88 **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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89
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90
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91 **Further reading**
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92
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93 - Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
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94 - Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf)
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95 - Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)
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96
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97 -----
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98
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99 **Grep Examples**
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100
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101 - **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**)
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102 - **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC
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103 - **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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104 - **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file.
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105 - **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
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106 - **hsa|mmu** would match lines containing "hsa" or "mmu" (or both).
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107
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108 -----
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109
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110 **Regular Expression Syntax**
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111
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112 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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113
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114 - **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
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115 - **^** matches the beginning of a string(but not an internal line).
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116 - **\\d** matches a digit, same as [0-9].
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117 - **\\D** matches a non-digit.
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118 - **\\s** matches a whitespace character.
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119 - **\\S** matches anything BUT a whitespace.
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120 - **\\t** matches a tab.
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121 - **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
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122 - **\\W** matches anything but an alphanumeric character.
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123 - **(** .. **)** groups a particular pattern.
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124 - **\\Z** matches the end of a string(but not a internal line).
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125 - **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
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126
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127 - **{n}** The preceding item is matched exactly n times.
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128 - **{n,}** The preceding item ismatched n or more times.
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129 - **{n,m}** The preceding item is matched at least n times but not more than m times.
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130
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131 - **[** ... **]** 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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132 - **.** Matches any single character except a newline.
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133 - ***** The preceding item will be matched zero or more times.
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134 - **?** The preceding item is optional and matched at most once.
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135 - **+** The preceding item will be matched one or more times.
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136 - **^** has two meaning:
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137 - matches the beginning of a line or string.
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138 - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
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139 - **$** matches the end of a line or string.
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140 - **\|** Separates alternate possibilities.
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141
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142
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143 </help>
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144 </tool>
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