Mercurial > repos > sjung > bdds
comparison fseq.xml @ 2:0ea254c514b7 draft
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| author | sjung |
|---|---|
| date | Wed, 24 May 2017 00:35:24 -0400 |
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| 1:29760e9a840b | 2:0ea254c514b7 |
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| 1 <tool id="fseq" name="FSeq" version="F-Seq: 1.85"> | |
| 2 <description>A Feature Density Estimator for High-Throughput Sequence Tags</description> | |
| 3 <requirements> | |
| 4 <requirement type="package">java</requirement> | |
| 5 <requirement type="package">fseq</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 <![CDATA[ | |
| 9 fseq -f $fragSize -l $featLen -of $outputFormat -s $wiggleTrackStep -t $threshold | |
| 10 #for $i, $j in enumerate($fd): | |
| 11 $j.input | |
| 12 #end for | |
| 13 ; cat *.bed > $output | |
| 14 ]]> | |
| 15 </command> | |
| 16 | |
| 17 <stdio> | |
| 18 <exit_code range="1:" level="fatal" description="Error" /> | |
| 19 </stdio> | |
| 20 | |
| 21 <inputs> | |
| 22 <repeat name="fd" title="bed format inputs" min="1"> | |
| 23 <param help="" label="input" name="input" type="data"/> | |
| 24 </repeat> | |
| 25 <param name="fragSize" type="integer" value="0" label="Fragment Size" /> | |
| 26 <param name="featLen" type="integer" value="600" label="feature length" /> | |
| 27 <param name="outputFormat" type="select" label="output format" > | |
| 28 <option value="wig">Wiggle</option> | |
| 29 <option value="bed">Bed</option> | |
| 30 <option value="npf">narrowPeak</option> | |
| 31 </param> | |
| 32 <param name="wiggleTrackStep" type="integer" value="1" label="wiggle track step" /> | |
| 33 <param name="threshold" type="float" value="4.0" label="threshold" /> | |
| 34 </inputs> | |
| 35 | |
| 36 <outputs> | |
| 37 <data format="bed,wig" label="${tool.name} on ${on_string}" name="output" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <help> | |
| 44 </help> | |
| 45 </tool> |