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1 <tool id="gops_merge_1" name="Merge">
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2 <description>the overlapping intervals of a dataset</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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6 </requirements>
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7 <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
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8 <inputs>
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9 <param format="interval" name="input1" type="data">
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10 <label>Merge overlaping regions of</label>
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11 </param>
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12 <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
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13 <label>Output 3 column bed</label>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data format="input" name="output" metadata_source="input1" />
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18 </outputs>
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19 <code file="operation_filter.py">
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20 <hook exec_after_process="exec_after_merge" />
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21 </code>
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22 <tests>
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23 <test>
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24 <param name="input1" value="1.bed" />
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25 <output name="output" file="gops-merge.dat" />
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26 <param name="returntype" value="true" />
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27 </test>
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28 <test>
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29 <param name="input1" value="2_mod.bed" ftype="interval"/>
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30 <output name="output" file="gops_merge_diffCols.dat" />
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31 <param name="returntype" value="true" />
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32 </test>
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33 <test>
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34 <param name="input1" value="gops_bigint.interval" />
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35 <output name="output" file="gops_merge_out2.bed" />
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36 <param name="returntype" value="true" />
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37 </test>
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38 </tests>
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39 <help>
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40
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41 .. class:: infomark
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42
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43 **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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44
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45 -----
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46
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47 **Screencasts!**
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48
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49 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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50
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51 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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52
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53 -----
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54
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55 This operation merges all overlapping intervals into single intervals.
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56
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57 **Example**
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58
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59 .. image:: ${static_path}/operation_icons/gops_merge.gif
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60
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61 </help>
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62 </tool> |
