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1 <tool id="fseq" name="FSeq" version="F-Seq: 1.85">
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2 <description>A Feature Density Estimator for High-Throughput Sequence Tags</description>
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3 <requirements>
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4 <requirement type="package">java</requirement>
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5 <requirement type="package">fseq</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 fseq -f $fragSize -l $featLen -of $outputFormat -s $wiggleTrackStep -t $threshold
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10 #for $i, $j in enumerate($fd):
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11 $j.input
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12 #end for
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13 ; cat *.bed > $output
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14 ]]>
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15 </command>
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16
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17 <stdio>
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18 <exit_code range="1:" level="fatal" description="Error" />
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19 </stdio>
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20
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21 <inputs>
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22 <repeat name="fd" title="bed format inputs" min="1">
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23 <param help="" label="input" name="input" type="data"/>
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24 </repeat>
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25 <param name="fragSize" type="integer" value="0" label="Fragment Size" />
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26 <param name="featLen" type="integer" value="600" label="feature length" />
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27 <param name="outputFormat" type="select" label="output format" >
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28 <option value="wig">Wiggle</option>
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29 <option value="bed">Bed</option>
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30 <option value="npf">narrowPeak</option>
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31 </param>
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32 <param name="wiggleTrackStep" type="integer" value="1" label="wiggle track step" />
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33 <param name="threshold" type="float" value="4.0" label="threshold" />
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34 </inputs>
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35
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36 <outputs>
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37 <data format="bed,wig" label="${tool.name} on ${on_string}" name="output" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 </test>
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42 </tests>
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43 <help>
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44 </help>
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45 </tool>
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