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