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1 <tool id="gops_basecoverage_1" name="Base Coverage" version="0.0.1">
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2 <description>of all intervals</description>
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3 <command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
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4 <requirements>
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5 <requirement type="package" version="0.7.1">bx-python</requirement>
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6 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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7 </requirements>
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8 <inputs>
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9 <param format="interval" name="input1" type="data">
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10 <label>Compute coverage for</label>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="output" />
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15 </outputs>
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16 <code file="operation_filter.py"/>
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17 <tests>
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18 <test>
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19 <param name="input1" value="1.bed" />
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20 <output name="output" file="gops_basecoverage_out.txt" />
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21 </test>
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22 <test>
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23 <param name="input1" value="gops_bigint.interval" />
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24 <output name="output" file="gops_basecoverage_out2.txt" />
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25 </test>
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26 </tests>
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27 <help>
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28
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29 .. class:: infomark
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30
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31 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
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32
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33 This operation counts the total bases covered by a set of intervals. Bases that are covered by more than one interval are **not** counted more than once towards the total.
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34
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35 -----
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36
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37 **Screencasts!**
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38
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39 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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40
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41 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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42
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43 **Example**
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44
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45 .. image:: ${static_path}/operation_icons/gops_baseCoverage.gif
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46
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47
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48 </help>
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49 </tool>
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