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comparison poretools_squiggle.xml @ 0:092fbeab151e 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 14:18:03 -0500
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children 1ac861671d76
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-1:000000000000 0:092fbeab151e
1 <?xml version="1.0"?>
2 <tool id="poretools_squiggle" name="Plot signals" version="@VERSION@.0">
3 <description>for 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 squiggle '$input' --saveas $extension --num-facets $num_facets
11 $theme_bw
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 <param name="num_facets" argument="--num-facets" type="integer" value="6" label="Number of plot facets" />
18 </inputs>
19 <outputs>
20 <data format="txt" name="output">
21 <discover_datasets pattern="__designation_and_ext__" directory="." visible="true" />
22 </data>
23 </outputs>
24 <tests>
25 <test>
26 <expand macro="test_input" />
27 <param name="extension" value="png" />
28 <output name="output">
29 <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.png" lines_diff="986" />
30 <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.png" lines_diff="883" />
31 </output>
32 </test>
33 <test>
34 <expand macro="test_input" />
35 <param name="extension" value="pdf" />
36 <output name="output">
37 <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.pdf" lines_diff="35" />
38 <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.pdf" lines_diff="35" />
39 </output>
40 </test>
41 </tests>
42 <help>
43 Plot the observed signals for FAST5 reads.
44 </help>
45 <expand macro="citations" />
46 </tool>