| Previous changeset 1:29760e9a840b (2017-05-24) Next changeset 3:43e4ba4796c1 (2017-05-24) |
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Commit message:
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added:
fseq.xml |
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| diff -r 29760e9a840b -r 0ea254c514b7 fseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fseq.xml Wed May 24 00:35:24 2017 -0400 |
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| @@ -0,0 +1,45 @@ +<tool id="fseq" name="FSeq" version="F-Seq: 1.85"> + <description>A Feature Density Estimator for High-Throughput Sequence Tags</description> + <requirements> + <requirement type="package">java</requirement> + <requirement type="package">fseq</requirement> + </requirements> + <command> +<![CDATA[ +fseq -f $fragSize -l $featLen -of $outputFormat -s $wiggleTrackStep -t $threshold +#for $i, $j in enumerate($fd): + $j.input +#end for +; cat *.bed > $output +]]> + </command> + + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + + <inputs> + <repeat name="fd" title="bed format inputs" min="1"> + <param help="" label="input" name="input" type="data"/> + </repeat> + <param name="fragSize" type="integer" value="0" label="Fragment Size" /> + <param name="featLen" type="integer" value="600" label="feature length" /> + <param name="outputFormat" type="select" label="output format" > + <option value="wig">Wiggle</option> + <option value="bed">Bed</option> + <option value="npf">narrowPeak</option> + </param> + <param name="wiggleTrackStep" type="integer" value="1" label="wiggle track step" /> + <param name="threshold" type="float" value="4.0" label="threshold" /> + </inputs> + + <outputs> + <data format="bed,wig" label="${tool.name} on ${on_string}" name="output" /> + </outputs> + <tests> + <test> + </test> + </tests> + <help> + </help> +</tool> |