<tool id="fileGrep1" name="Match">
  <description>a column from one Query against another Query</description>
  <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command>
  <inputs>
    <param name="col" size="2" type="text" value="1" label="Match content of column"/>
    <param format="tabular" name="input1" type="data" label="From Query1"/>
    <param format="tabular" name="input2" type="data" label="Against Query2"/>
    <param name="match" type="select" label="and return rows that">
      <option value="">Match</option>
      <option value="-v">Do not match</option>
    </param>
  </inputs>
  <outputs>
    <data format="input" name="out_file1" metadata_source="input2" />
  </outputs>
  <help>
This tool is based on UNIX command grep with option -f. It matches content of one query against another. For example, assume you have two queries - one that contains EST accession numbers and some other information::

  AA001229	12	12
  A001501	7	7
  AA001641	6	6
  AA001842	6	6
  AA002047	6	6
  AA004638	3	3

and another that is a typical BED file describing genomic location of some ESTs::

  chr7 115443235 115443809 CA947954_exon_0_0_chr7_115443236_f 0	+
  chr7 115443236 115443347 DB338189_exon_0_0_chr7_115443237_f 0	+
  chr7 115443347 115443768 DB338189_exon_1_0_chr7_115443348_f 0	+
  chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0	+
  chr7 115443243 115443347 DB331869_exon_0_0_chr7_115443244_f 0	+
  chr7 115443347 115443373 DB331869_exon_1_0_chr7_115443348_f 0	+

Using this tool you will be able to tell how many ESTs in Query1 are also preset in Query2 and will output this::

  chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0	

if **Match** option is chosen.

</help>
</tool>