Mercurial > repos > xuebing > sharplabtool
comparison tools/unix_tools/word_list_grep.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="cshl_word_list_grep" name="Select lines"> | |
2 <description>by word list</description> | |
3 <command interpreter="perl"> | |
4 word_list_grep.pl | |
5 #if $searchwhere.choice == "column": | |
6 -c $searchwhere.column | |
7 #end if | |
8 -o $output | |
9 $inverse | |
10 $caseinsensitive | |
11 $wholewords | |
12 $skip_first_line | |
13 $wordlist | |
14 $input | |
15 </command> | |
16 | |
17 <inputs> | |
18 <param name="input" format="txt" type="data" label="input file" /> | |
19 <param name="wordlist" format="txt" type="data" label="word list file" /> | |
20 | |
21 | |
22 <param name="inverse" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Inverse filter" | |
23 help="Report lines NOT matching the word list" /> | |
24 | |
25 <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search" | |
26 help="" /> | |
27 | |
28 <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words" | |
29 help="ignore partial matches (e.g. 'apple' will not match 'snapple') " /> | |
30 | |
31 <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line" | |
32 help="Select this option if the first line contains column headers. First line will not be filtered. " /> | |
33 | |
34 <conditional name="searchwhere"> | |
35 <param name="choice" type="select" label="Search words in"> | |
36 <option value="line" selected="true">entire line</option> | |
37 <option value="column">specific column</option> | |
38 </param> | |
39 | |
40 <when value="line"> | |
41 </when> | |
42 | |
43 <when value="column"> | |
44 <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" /> | |
45 </when> | |
46 </conditional> | |
47 | |
48 </inputs> | |
49 | |
50 <outputs> | |
51 <data name="output" format="input" metadata_source="input" /> | |
52 </outputs> | |
53 | |
54 <help> | |
55 **What it does** | |
56 | |
57 This tool selects lines that match words from a word list. | |
58 | |
59 -------- | |
60 | |
61 **Example** | |
62 | |
63 Input file (UCSC's rmsk track from dm3):: | |
64 | |
65 585 787 66 241 11 chrXHet 2860 3009 -201103 - DNAREP1_DM LINE Penelope 0 594 435 1 | |
66 585 1383 78 220 0 chrXHet 3012 3320 -200792 - DNAREP1_DM LINE Penelope -217 377 2 1 | |
67 585 244 103 0 0 chrXHet 3737 3776 -200336 - DNAREP1_DM LINE Penelope -555 39 1 1 | |
68 585 2270 83 144 0 chrXHet 7907 8426 -195686 + DNAREP1_DM LINE Penelope 1 594 0 1 | |
69 585 617 189 73 68 chrXHet 10466 10671 -193441 + DNAREP1_DM LINE Penelope 368 573 -21 1 | |
70 586 1122 71 185 0 chrXHet 173138 173322 -30790 - PROTOP DNA P -4033 447 230 1 | |
71 ... | |
72 ... | |
73 | |
74 | |
75 Word list file:: | |
76 | |
77 STALKER | |
78 PROTOP | |
79 | |
80 | |
81 | |
82 Output sequence (searching in column 11):: | |
83 | |
84 586 1122 71 185 0 chrXHet 173138 173322 -30790 - PROTOP DNA P -4033 447 230 1 | |
85 586 228 162 0 0 chrXHet 181026 181063 -23049 + STALKER4_I LTR Gypsy 9 45 -6485 1 | |
86 585 245 105 26 0 chr3R 41609 41647 -27863406 + PROTOP_B DNA P 507 545 -608 4 | |
87 586 238 91 0 0 chr3R 140224 140257 -27764796 - PROTOP_B DNA P -617 536 504 4 | |
88 ... | |
89 ... | |
90 | |
91 ( With **find whole-words** not selected, *PROTOP* matched *PROTOP_B*, *STALKER* matched *STALKER4_I* ) | |
92 | |
93 | |
94 | |
95 | |
96 Output sequence (searching in column 11, and whole-words only):: | |
97 | |
98 586 670 90 38 57 chrXHet 168356 168462 -35650 - PROTOP DNA P -459 4021 3918 1 | |
99 586 413 139 70 0 chrXHet 168462 168548 -35564 - PROTOP DNA P -3406 1074 983 1 | |
100 586 1122 71 185 0 chrXHet 173138 173322 -30790 - PROTOP DNA P -4033 447 230 1 | |
101 ... | |
102 ... | |
103 | |
104 </help> | |
105 | |
106 </tool> |