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1 <tool id="clippolya" name="ClipPolyA">
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2 <command >
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3 <![CDATA[
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4 java -Xmx4g -jar /home/galaxy/galaxy-dist/tools/ngs_rna/PolyA/ClipPolyA.jar -i $input -o $output -s $minSignalLength -m $minReadLength $outputAll $threePrime $fivePrime $polyASignals $polyTSignals
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5 ]]>
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6 </command>
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7 <inputs>
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8 <param name="input" type="data" format="fastqsanger" label="Fastq file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
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9 <param type="integer" value="6" name="minSignalLength" label="Min poly-A/T signal length"/>
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10 <param type="integer" value="25" name="minReadLength" label="Min read length after clipping"/>
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11 <param name="outputAll" type="boolean" checked="true" truevalue="-k" falsevalue="" label="Output all reads (clipped and non-clipped)" help="If not selected, only clipped sequences were written to output" />
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12 <param name="threePrime" type="boolean" checked="true" truevalue="-3" falsevalue="" label="Clip from 3'-end" />
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13 <param name="fivePrime" type="boolean" checked="false" truevalue="-5" falsevalue="" label="Clip from 5'-end" />
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14 <param name="polyASignals" type="boolean" checked="true" truevalue="-a" falsevalue="" label="Poly-A signals" />
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15 <param name="polyTSignals" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Poly-T signals" />
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16
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="fastqsanger" label="Poly-A trimmed on ${on_string}"/>
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20 </outputs>
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21 <help>
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22
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23 Implemented by Alexander Graf
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24
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25 **What it does**
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26 Poly-A and Poly-T signals are trimmed from the beginning or the ending of a read, where the signal occures at least 6 times.
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27
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28 ------
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29
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30 **Input formats**
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31
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32 FASTQ file in Sanger format
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33
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34 ------
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35
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36 **Output**
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37
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38 FASTQ file containing the clipped reads
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39
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40 </help>
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41 </tool>
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