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42 lines
1.7 KiB
XML
42 lines
1.7 KiB
XML
<tool id="fileGrep1" name="Match" version="1.0.0">
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<description>a column from one Query against another Query</description>
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<command>cut -f $col $input1 | grep -f - $match $input2 > $out_file1</command>
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<inputs>
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<param name="col" size="2" type="text" value="1" label="Match content of column"/>
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<param format="tabular" name="input1" type="data" label="From Query1"/>
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<param format="tabular" name="input2" type="data" label="Against Query2"/>
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<param name="match" type="select" label="and return rows that">
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<option value="">Match</option>
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<option value="-v">Do not match</option>
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</param>
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</inputs>
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<outputs>
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<data format="input" name="out_file1" metadata_source="input2" />
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</outputs>
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<help>
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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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AA001229 12 12
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A001501 7 7
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AA001641 6 6
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AA001842 6 6
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AA002047 6 6
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AA004638 3 3
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and another that is a typical BED file describing genomic location of some ESTs::
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chr7 115443235 115443809 CA947954_exon_0_0_chr7_115443236_f 0 +
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chr7 115443236 115443347 DB338189_exon_0_0_chr7_115443237_f 0 +
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chr7 115443347 115443768 DB338189_exon_1_0_chr7_115443348_f 0 +
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chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0 +
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chr7 115443243 115443347 DB331869_exon_0_0_chr7_115443244_f 0 +
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chr7 115443347 115443373 DB331869_exon_1_0_chr7_115443348_f 0 +
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Using this tool you will be able to tell how many ESTs in Query1 are also preset in Query2 and will output this::
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chr7 115443239 115443802 AA001842_exon_0_0_chr7_115443240_f 0
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if **Match** option is chosen.
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</help>
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</tool> |