Mercurial > repos > iuc > poretools_qualpos

comparison poretools_qualpos.xml @ 0:a4d55649f809 draft

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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 14:21:32 -0500
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children 10de42827db9
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-1:000000000000 0:a4d55649f809
1 <?xml version="1.0"?>
2 <tool id="poretools_qualpos" name="Generate box-whisker" version="@VERSION@.0">
3 <description>plot of quality score distribution over positions in nanopore reads</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="aggressive">
9 <![CDATA[
10 poretools qualpos '$input' --saveas qualpos.$extension --min-length $min_length
11 --max-length $max_length --bin-width $bin_width $theme_bw && mv qualpos.$extension '$output'
12 ]]>
13 </command>
14 <inputs>
15 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
16 <expand macro="plot_options">
17 <option value="pdf">PDF</option>
18 <option value="svg">SVG</option>
19 </expand>
20 <param name="theme_bw" argument="--theme-bw" type="boolean" truevalue="--theme-bw" falsevalue="" label="Use a monochrome color " />
21 <expand macro="length_options" />
22 <param name="bin_width" argument="--bin-width" type="integer" value="1000" label="The width of bins" />
23 </inputs>
24 <outputs>
25 <expand macro="image_output">
26 <when input="extension" value="svg" format="svg" />
27 </expand>
28 </outputs>
29 <tests>
30 <test>
31 <expand macro="test_input" />
32 <param name="extension" value="png" />
33 <output name="output" file="poretools-qualpos-out1.png" ftype="png" lines_diff="195" />
34 </test>
35 <test>
36 <expand macro="test_input" />
37 <param name="extension" value="pdf" />
38 <output name="output" file="poretools-qualpos-out1.pdf" ftype="pdf" lines_diff="36" />
39 </test>
40 </tests>
41 <help>
42 Produce a box-whisker plot of quality score distribution over positions in nanopore reads
43 </help>
44 <expand macro="citations" />
45 </tool>