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1 <tool id="paired_end_cross_plot" name="Paired-end cross plot" version="1.0.0">
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2 <description></description>
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3 <command>
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4 <![CDATA[
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5 java -jar $__tool_directory__/pairedendCrossPlot.jar
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6 -f "$input1"
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7 -r "$input2"
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8 -w $window_size
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9 -o "$output" 1>/dev/null
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10 ]]>
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11 </command>
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12 <inputs>
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13 <param name="input1" type="data" format="scidx" label="Read 1 ScIdx file" />
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14 <param name="input2" type="data" format="scidx" label="Read 2 ScIdx file" />
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15 <param name="window_size" type="integer" value="500" min="1" label="Size of window upstream and downstream around the reference point in base pairs" />
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16 </inputs>
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17 <outputs>
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18 <data name="output" format="tabular" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input1" value="input1.scidx" ftype="scidx"/>
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23 <param name="input2" value="input2.scidx" ftype="scidx"/>
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24 <param name="window_size" value="500"/>
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25 <output name="output" file="output1.tabular" ftype="tabular"/>
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26 </test>
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27 <test>
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28 <param name="input1" value="input3.scidx" ftype="scidx"/>
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29 <param name="input2" value="input4.scidx" ftype="scidx"/>
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30 <param name="window_size" value="500"/>
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31 <output name="output" file="output2.tabular" ftype="tabular"/>
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32 </test>
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33 </tests>
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34 <help>
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35
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36 **What it does**
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37
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38 Produces a frequency histogram of the relative occurrence of Read2 5' ends relative to the
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39 start of every Read1 5' end in a user-specified coordinate window.
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40
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41 -----
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42
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43 **Options**
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44
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45 * **Window Size** - sets the size of the window upstream and downstream around the reference point in base pairs.
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46
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47 </help>
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48 <citations>
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49 <citation type="bibtex">
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50 @unpublished{None,
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51 author = {Lai, William},
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52 title = {None},
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53 year = {None},
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54 eprint = {None},
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55 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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56 }</citation>
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57 </citations>
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58 </tool>
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