root/galaxy-central/tools/filters/fileGrep.xml

リビジョン 2, 1.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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>
17This 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
26and 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
35Using this tool you will bne 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
39if **Match** option is chosen.
40
41</help>
42</tool>
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