Mercurial > repos > iuc > poretools_occupancy

annotate poretools_occupancy.xml @ 1:dc53931f6952 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
author iuc
date Sun, 19 Jan 2020 14:04:47 +0000
parents 2c6bea49d2ab
children 0b5cfa9e7418
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2c6bea49d2ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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1 <?xml version="1.0"?>
1
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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2 <tool id="poretools_occupancy" name="Plot performance" version="@VERSION@.1">
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3 <description>per cell in nanopore reads</description>
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4 <macros>
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5 <import>macros.xml</import>
2c6bea49d2ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive">
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9 <![CDATA[
1
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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10 @MPLBACKEND@
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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11 poretools occupancy
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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12 '$input'
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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13 --saveas occupancy.$extension
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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14 --plot-type $plot_type
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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15 &&
dc53931f6952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
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16 mv occupancy.$extension '$output'
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2c6bea49d2ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
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21 <param name="extension" type="select" label="File format for histogram">
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22 <option value="png">PNG</option>
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23 <option value="pdf">PDF</option>
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24 <option value="svg">SVG</option>
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25 </param>
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26 <param name="plot_type" argument="--plot-type" type="select" label="Plot type to generate">
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27 <option value="read_count">Read count</option>
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28 <option value="total_bp">Total base pairs</option>
2c6bea49d2ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <expand macro="image_output" />
2c6bea49d2ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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33 </outputs>
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34 <tests>
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35 <test>
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36 <expand macro="test_input" />
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37 <param name="extension" value="png" />
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38 <param name="plot_type" value="read_count" />
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39 <output name="output" file="poretools-occupancy-out1.png" ftype="png" compare="sim_size" />
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40 </test>
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41 <test>
2c6bea49d2ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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42 <expand macro="test_input" />
2c6bea49d2ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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43 <param name="extension" value="pdf" />
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44 <param name="plot_type" value="total_bp" />
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45 <output name="output" file="poretools-occupancy-out1.pdf" ftype="pdf" lines_diff="384" />
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46 </test>
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47 </tests>
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48 <help>
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49 Plot the throughput performance of each pore on the flowcell during a given sequencing run.
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50 </help>
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51 <expand macro="citations" />
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52 </tool>