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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 be 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> |
