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1 <tool id="bowtie2bed" name="bowtie-to-bed">
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2 <description> converter and read extender</description>
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3 <command interpreter="perl">bowtie2bed.pl $input $out_file1 $extendLength </command>
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4 <inputs>
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5 <param name="input" format="txt" type="data" label="Bowtie map result file"/>
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6 <param name="extendLength" size="10" type="integer" value="200" label="Extend 3 primer (bp)"/>
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7 </inputs>
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8 <outputs>
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9 <data format="bed" name="out_file1" />
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10 </outputs>
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11 <tests>
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12 <test>
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13 <param name="input" value="test.map" ftype="TXT"/>
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14 <param name="extendLength" value="200"/>
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15 <output name="out_file1" file="testmap.bed"/>
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16 </test>
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17 </tests>
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18 <help>
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19
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20
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21 **What it does**
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22
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23 This tool converts bowtie output map format file to bed format, with the option to extend the 3 primer end.
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24
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25 - Sequence and quality information is lost after conversion
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26 - The output contains a track name at the first row
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27
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28 -----
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29
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30 **Example**
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31
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32 Converting the following bowtie mapped reads::
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33
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34 SRR073078.2 HWUSI-EAS465_8_1_1_524 length=36 - chr2 112499209 AGTGTGACTGCATCTCTTCCTTCGTGGGGCTNCAGT ...
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35 SRR073078.3 HWUSI-EAS465_8_1_1_1054 length=36 + chr17 75877120 CCACNCCTCCTTTCAAAACACACTGCCAGGTGCGTC ...
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36
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37 will result in::
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38
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39 track name=/home/xuebing/Research/galaxy/galaxy-dist/database/files/000/dataset_5.dat itemRgb=On
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40 chr2 112499109 112499245 SRR073078.2-HWUSI-EAS465_8_1_1_524-length=36 1 - 112499209 112499245 0,255,0
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41 chr17 75877120 75877256 SRR073078.3-HWUSI-EAS465_8_1_1_1054-length=36 1 + 75877120 75877156 255,0,0
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42
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43 </help>
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44 </tool>
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