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comparison tools/filters/fileGrep.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="fileGrep1" name="Match">
2 <description>a column from one Query against another Query</description>
3 <command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command>
4 <inputs>
5 <param name="col" size="2" type="text" value="1" label="Match content of column"/>
6 <param format="tabular" name="input1" type="data" label="From Query1"/>
7 <param format="tabular" name="input2" type="data" label="Against Query2"/>
8 <param name="match" type="select" label="and return rows that">
9 <option value="">Match</option>
10 <option value="-v">Do not match</option>
11 </param>
12 </inputs>
13 <outputs>
14 <data format="input" name="out_file1" metadata_source="input2" />
15 </outputs>
16 <help>
17 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::
18
19 AA001229 12 12
20 A001501 7 7
21 AA001641 6 6
22 AA001842 6 6
23 AA002047 6 6
24 AA004638 3 3
25
26 and another that is a typical BED file describing genomic location of some ESTs::
27
28 chr7 115443235 115443809 CA947954_exon_0_0_chr7_115443236_f 0 +
29 chr7 115443236 115443347 DB338189_exon_0_0_chr7_115443237_f 0 +
30 chr7 115443347 115443768 DB338189_exon_1_0_chr7_115443348_f 0 +
31 chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0 +
32 chr7 115443243 115443347 DB331869_exon_0_0_chr7_115443244_f 0 +
33 chr7 115443347 115443373 DB331869_exon_1_0_chr7_115443348_f 0 +
34
35 Using this tool you will be able to tell how many ESTs in Query1 are also preset in Query2 and will output this::
36
37 chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0
38
39 if **Match** option is chosen.
40
41 </help>
42 </tool>