Mercurial > repos > iuc > poretools_squiggle
comparison poretools_squiggle.xml @ 0:ce8af9373061 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
author | iuc |
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date | Tue, 19 Dec 2017 14:49:34 -0500 |
parents | |
children | 34553d0caa5e |
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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> |