Mercurial > repos > iuc > poretools_yield_plot

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
author iuc
date Tue, 19 Dec 2017 14:22:25 -0500
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a8c8a7354ab7 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"?>
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2 <tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.0">
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3 <description>of sequencing yield over time</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive">
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9 <![CDATA[
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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10 poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type
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11 $theme_bw
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12 #if $skip != '0':
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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13 --skip $skip
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14 #end if
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15 && mv plot.$extension '$output'
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16 ]]>
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17 </command>
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18 <inputs>
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19 <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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20 <param name="plot_type" argument="--plot-type" type="select" label="Plot reads or base pairs">
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21 <option value="reads">Reads</option>
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22 <option value="basepairs">Base pairs</option>
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23 </param>
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24 <param argument="--skip" type="integer" value="0" label="Plot only every nth point" help="Increases performance at the cost of resolution." />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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25 <expand macro="plot_options" />
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26 </inputs>
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27 <outputs>
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28 <expand macro="image_output" />
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29 </outputs>
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30 <tests>
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31 <test>
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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32 <expand macro="test_input" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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33 <param name="extension" value="png" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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34 <param name="plot_type" value="reads" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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35 <output name="output" file="poretools-yield-plot-out1.png" ftype="png" lines_diff="301" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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36 </test>
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37 <test>
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38 <expand macro="test_input" />
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39 <param name="extension" value="svg" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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40 <param name="plot_type" value="basepairs" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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41 <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="40" />
a8c8a7354ab7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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42 </test>
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43 </tests>
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44 <help>
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45 Create a collector’s curve reflecting the sequencing yield over time.
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46 </help>
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47 <expand macro="citations" />
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48 </tool>