root/galaxy-central/tools/unix_tools/word_list_grep.xml @ 3

<tool id="cshl_word_list_grep" name="Select lines">
<description>by word list</description>
<command interpreter="perl">
        word_list_grep.pl 
        #if $searchwhere.choice == "column":
                -c $searchwhere.column
        #end if
        -o $output 
        $inverse 
        $caseinsensitive 
        $wholewords 
        $skip_first_line
        $wordlist 
        $input
</command>

<inputs>
        <param name="input" format="txt" type="data" label="input file" />
        <param name="wordlist" format="txt" type="data" label="word list file" />


        <param name="inverse" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Inverse filter" 
                help="Report lines NOT matching the word list" />

        <param name="caseinsensitive" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Case-Insensitive search" 
                help="" />

        <param name="wholewords" type="boolean" checked="false" truevalue="-w" falsevalue="" label="find whole-words" 
                help="ignore partial matches (e.g. 'apple' will not match 'snapple') " />

        <param name="skip_first_line" type="boolean" checked="false" truevalue="-s" falsevalue="" label="Ignore first line" 
                help="Select this option if the first line contains column headers. First line will not be filtered. " />

        <conditional name="searchwhere">
                <param name="choice" type="select" label="Search words in">
                        <option value="line" selected="true">entire line</option>
                        <option value="column">specific column</option>
                </param>

                <when value="line">
                </when>

                <when value="column">
                        <param name="column" label="in column" type="data_column" data_ref="input" accept_default="true" />
                </when>
        </conditional>

</inputs>

<outputs>
        <data name="output" format="input" metadata_source="input" />
</outputs>

<help>
**What it does**

This tool selects lines that match words from a word list.

--------

**Example**

Input file (UCSC's rmsk track from dm3)::

    585 787     66      241     11      chrXHet 2860    3009    -201103 -       DNAREP1_DM      LINE    Penelope        0       594     435     1
    585 1383    78      220     0       chrXHet 3012    3320    -200792 -       DNAREP1_DM      LINE    Penelope        -217    377     2       1
    585 244     103     0       0       chrXHet 3737    3776    -200336 -       DNAREP1_DM      LINE    Penelope        -555    39      1       1
    585 2270    83      144     0       chrXHet 7907    8426    -195686 +       DNAREP1_DM      LINE    Penelope        1       594     0       1
    585 617     189     73      68      chrXHet 10466   10671   -193441 +       DNAREP1_DM      LINE    Penelope        368     573     -21     1
    586 1122    71      185     0       chrXHet 173138  173322  -30790  -       PROTOP  DNA     P       -4033   447     230     1
    ...
    ...


Word list file::

  STALKER
  PROTOP

 

Output sequence (searching in column 11)::

    586 1122    71      185     0       chrXHet 173138  173322  -30790          -       PROTOP  DNA     P       -4033   447     230     1
    586 228     162     0       0       chrXHet 181026  181063  -23049          +       STALKER4_I      LTR     Gypsy   9       45      -6485   1
    585 245     105     26      0       chr3R   41609   41647   -27863406       +       PROTOP_B        DNA     P       507     545     -608    4
    586 238     91      0       0       chr3R   140224  140257  -27764796       -       PROTOP_B        DNA     P       -617    536     504     4
    ...
    ...

( With **find whole-words** not selected, *PROTOP* matched *PROTOP_B*, *STALKER* matched *STALKER4_I* )




Output sequence (searching in column 11, and whole-words only)::

    586 670     90      38      57      chrXHet 168356  168462  -35650  -       PROTOP  DNA     P       -459    4021    3918    1
    586 413     139     70      0       chrXHet 168462  168548  -35564  -       PROTOP  DNA     P       -3406   1074    983     1
    586 1122    71      185     0       chrXHet 173138  173322  -30790  -       PROTOP  DNA     P       -4033   447     230     1
    ...
    ...

</help>

</tool>