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annotate resample.xml @ 5:a64dc31ab7f2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 39a0176dab234a07118a79ac44ca7d79469d3b91"
author iuc
date Thu, 23 Jan 2020 07:27:22 -0500
parents 014a21767ac4
children df7356989ac1
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014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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1 <?xml version="1.0"?>
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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2 <tool id="circos_resample" name="Circos: Resample 1/2D data" version="@WRAPPER_VERSION@">
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3 <description>reduce numbers of points in a dataset before plotting</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 resample
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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10 -bin '$bins'
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11 $method
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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12 < '$input' | sed 's/ /\t/g' > '$output'
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13 ]]></command>
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14 <inputs>
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15 <param name="input" type="data" format="tabular" label="1D/2D Data track"/>
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16 <param name="bins" type="integer" value="1000000" min="1" label="Bin size" />
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17
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18 <param name="method" type="select" label="Summarization method">
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19 <option value="-avg">[2D] Average</option>
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20 <option value="-min">[2D] Minimum value in bin</option>
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21 <option value="-max">[2D] Maximum value in bin</option>
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22 <option value="-sum">[2D] Sum of values in bin</option>
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23 <option value="-count">[1D] Count bins</option>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="tabular" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input" value="resample/1.tab" ftype="tabular" />
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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32 <param name="bins" value="10000000" />
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33 <output name="output" file="resample/1.out" ftype="tabular" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 From the script's documentation:
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38
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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39 The data resolution in a figure is limited by the output print, or screen,
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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40 resolution and our own visual acuity.
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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41
014a21767ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
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42 To read more about how these limits affect figure design, see
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43 `this page <http://mkweb.bcgsc.ca/images/resolution/visual-acuity-sequence-visualization.pdf>`__
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44
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45 This script is designed to convert very high-resolution data tracks to
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46 low-resolution equivalents which are easier to interpret and faster to
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47 draw.
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48
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>