annotate poretools_qualpos.xml @ 1:4fe6b96aff72 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
author iuc
date Sun, 19 Jan 2020 09:07:34 -0500
parents 2e22ebec211a
children 626b6c2be5c2
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2e22ebec211a 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_qualpos" name="Generate box-whisker" version="@VERSION@.1">
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2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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3 <description>plot of quality score distribution over positions in nanopore reads</description>
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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4 <macros>
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5 <import>macros.xml</import>
2e22ebec211a 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" />
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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10 @MPLBACKEND@
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11 poretools qualpos '$input' --saveas qualpos.$extension --min-length $min_length --max-length $max_length --bin-width $bin_width $theme_bw && mv qualpos.$extension '$output'
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12 ]]>
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13 </command>
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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14 <inputs>
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15 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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16 <expand macro="plot_options">
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17 <option value="pdf">PDF</option>
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18 <option value="svg">SVG</option>
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19 </expand>
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20 <param name="theme_bw" argument="--theme-bw" type="boolean" truevalue="--theme-bw" falsevalue="" label="Use a monochrome color " />
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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21 <expand macro="length_options" />
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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22 <param name="bin_width" argument="--bin-width" type="integer" value="1000" label="The width of bins" />
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23 </inputs>
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24 <outputs>
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25 <expand macro="image_output">
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26 <when input="extension" value="svg" format="svg" />
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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27 </expand>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <expand macro="test_input" />
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32 <param name="extension" value="png" />
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33 <output name="output" file="poretools-qualpos-out1.png" ftype="png" compare="sim_size" />
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34 </test>
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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35 <test>
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36 <expand macro="test_input" />
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37 <param name="extension" value="pdf" />
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38 <output name="output" file="poretools-qualpos-out1.pdf" ftype="pdf" lines_diff="36" />
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39 </test>
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40 </tests>
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41 <help>
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42 Produce a box-whisker plot of quality score distribution over positions in nanopore reads
2e22ebec211a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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43 </help>
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44 <expand macro="citations" />
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45 </tool>