Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/galaxy/modifyFasta.xml @ 2:7c697a8bde9f

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author yufei-luo
date Thu, 17 Jan 2013 11:02:49 -0500
parents e0f8dcca02ed
children
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 <tool id="modifyFasta" name="modify fasta">
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2 <description>Extend or shring a list of sequences.</description>
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3 <command interpreter="python"> ../Java/Python/modifyFasta.py -i $inputFile
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4 #if $OptionStart.start == "Yes":
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5 -s $OptionStart.startValue
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6 #end if
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7
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8 #if $OptionEnd.end == "Yes":
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9 -e $OptionEnd.endValue
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10 #end if
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11 -o $outputFile
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12
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13 </command>
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14
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15
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16 <inputs>
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17 <param name="inputFile" type="data" label="Input fasta File" format="fasta"/>
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18 <conditional name="OptionStart">
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19 <param name="start" type="select" label="keep first nucleotides">
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20 <option value="Yes">Yes</option>
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21 <option value="No" selected="true">No</option>
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 </param>
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23 <when value="Yes">
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24 <param name="startValue" type="integer" value="0"/>
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25 </when>
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26 <when value="No">
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27 </when>
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28 </conditional>
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29
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30 <conditional name="OptionEnd">
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31 <param name="end" type="select" label="keep last nucleotides">
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32 <option value="Yes">Yes</option>
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33 <option value="No" selected="true">No</option>
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34 </param>
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35 <when value="Yes">
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36 <param name="endValue" type="integer" value="0"/>
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37 </when>
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38 <when value="No">
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39 </when>
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40 </conditional>
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41 </inputs>
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42
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43 <outputs>
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44 <data format="fasta" name="outputFile" label="[modifyFasta] Output File"/>
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45 </outputs>
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46
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47 <help>
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48 </help>
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49 </tool>