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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:51:08 -0400
parents 1e9d95cae35f
children
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1
72e1fdd8e7ae Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="gops_merge_1" name="Merge" version="1.0.0">
5
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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2 <description>the overlapping intervals of a dataset</description>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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3 <macros>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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4 <import>macros.xml</import>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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5 </macros>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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6 <expand macro="requirements" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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7 <code file="operation_filter.py">
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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8 <hook exec_after_process="exec_after_merge" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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9 </code>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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10 <command><![CDATA[
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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11 python '$__tool_directory__/gops_merge.py'
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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12 '$input1'
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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13 '$output'
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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14 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 $returntype
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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16 ]]></command>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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17 <inputs>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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18 <param name="input1" type="data" format="interval" label="Merge overlapping regions of" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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19 <param name="returntype" type="boolean" truevalue="-3" falsevalue="" label="Output 3 column bed" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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20 </inputs>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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21 <outputs>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 <data name="output" format_source="input1" metadata_source="input1" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 </outputs>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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24 <tests>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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25 <test>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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26 <param name="input1" value="1.bed" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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27 <param name="returntype" value="true" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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28 <output name="output" file="gops-merge.dat" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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29 </test>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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30 <test>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 <param name="input1" value="2_mod.bed" ftype="interval"/>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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32 <param name="returntype" value="true" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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parents: 2
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33 <output name="output" file="gops_merge_diffCols.dat" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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34 </test>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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35 <test>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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parents: 2
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36 <param name="input1" value="gops_bigint.interval" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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37 <param name="returntype" value="true" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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38 <output name="output" file="gops_merge_out2.bed" />
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 </test>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 </tests>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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41 <help><![CDATA[
0
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42 .. class:: infomark
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43
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44 **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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45
5
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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46 @SCREENCASTS@
0
10ac6097acdb Imported from capsule None
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47
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48 This operation merges all overlapping intervals into single intervals.
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49
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50 **Example**
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51
2
1e9d95cae35f Added tool image.
devteam <devteam@galaxyproject.org>
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52 .. image:: gops_merge.gif
5
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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53 ]]></help>
dfbbc0291b36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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54 </tool>