Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/galaxy/getWigData.xml @ 4:1fc014126d55

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author yufei-luo
date Fri, 18 Jan 2013 04:45:50 -0500
parents e0f8dcca02ed
children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
1 <tool id="getWigData" name="get wig data">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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2 <description>Compute the average data for some genomic coordinates using WIG files</description>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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3 <command interpreter="python">
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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4 ../Java/Python/getWigData.py -i $inputGff3File -f gff3 -w $inputWigFile -t $tagName -$strand -o $outputFile
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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5 </command>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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7 <inputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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8 <param name="inputGff3File" type="data" label="Input Gff3 File (compulsory option)" format="gff3"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
9 <param name="inputWigFile" type="data" label="Input Wig File (compulsory option)" format="wig"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
10 <param name="tagName" type="text" value="None" label="tag option (compulsory option)" help="choose a tag name to write the wig information to output file."/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
11 <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="consider both strands separately."/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
12 </inputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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13
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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14 <outputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff changeset
15 <data format="gff3" name="outputFile" label="[getWigData -> gff3] Output File"/>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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16 </outputs>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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17 </tool>