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/tools/filters/fileGrep.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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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>
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 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
39if **Match** option is chosen.
40
41</help>
42</tool>