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