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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:38:23 -0400
parents a3c7fd2ae338
children
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1
8f2c476e92ed Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="gops_complement_1" name="Complement" version="1.0.0">
5
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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2 <description>intervals of a dataset</description>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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3 <macros>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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4 <import>macros.xml</import>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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5 </macros>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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6 <expand macro="requirements" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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7 <code file="operation_filter.py"/>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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8 <command><![CDATA[
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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9 python '$__tool_directory__/gops_complement.py'
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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10 '$input1'
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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11 '$output'
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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12 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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13 -l '${chromInfo}'
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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14 $allchroms
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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15 ]]></command>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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16 <inputs>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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17 <param name="input1" type="data" format="interval" label="Complement regions of" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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18 <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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19 </inputs>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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20 <outputs>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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21 <data name="output" format_source="input1" metadata_source="input1" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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22 </outputs>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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23 <tests>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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24 <test>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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25 <param name="input1" value="1.bed" dbkey="hg17" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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26 <param name="allchroms" value="true" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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27 <output name="output" file="gops_complement_out.bed" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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28 </test>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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29 <test>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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30 <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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31 <param name="allchroms" value="true" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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32 <output name="output" file="gops_complement_out_diffCols.dat" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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33 </test>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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34 <test>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
parents: 2
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35 <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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36 <param name="allchroms" value="true" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
devteam
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37 <output name="output" file="gops_complement_out2.bed" />
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 </test>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 </tests>
1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 <help><![CDATA[
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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 This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval.
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46
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1377a23bc02a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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47 @SCREENCASTS@
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48
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49 **Syntax**
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50
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51 - **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the dataset.
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52
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53 -----
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54
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55 **Example**
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56
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a3c7fd2ae338 Added tool image.
Dave Bouvier <dave@bx.psu.edu>
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57 .. image:: gops_complement.gif
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58 ]]></help>
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59 </tool>