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comparison poretools_events.xml @ 1:28d7819c312f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
author iuc
date Sun, 19 Jan 2020 09:10:59 -0500
parents 1d835c691480
children
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0:1d835c691480 1:28d7819c312f
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.0"> 2 <tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.1">
3 <description>from a set of sequencing reads</description> 3 <description>from a set of sequencing reads</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
10 poretools events $precalled '$input' > '$output' 10 poretools events $precalled '$input' > '$output'
11 ]]> 11 ]]>
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> 14 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
15 <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="--pre-basecalled" label="Report pre-basecalled events" /> 15 <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="" label="Report pre-basecalled events" />
16 </inputs> 16 </inputs>
17 <outputs> 17 <outputs>
18 <data name="output" format="tabular" /> 18 <data name="output" format="tabular" />
19 </outputs> 19 </outputs>
20 <tests> 20 <tests>
21 <test> 21 <test>
22 <expand macro="test_input" /> 22 <expand macro="test_input" />
23 <param name="precalled" value="false" /> 23 <param name="precalled" value="false" />
24 <output name="output" file="poretools-events-out1.tabular" ftype="tabular" /> 24 <output name="output" ftype="tabular">
25 <assert_contents>
26 <has_n_lines n="2901"/>
27 <has_text text="template"/>
28 <has_text text="complement"/>
29 <not_has_text text="pre_basecalled"/>
30 </assert_contents>
31 </output>
25 </test> 32 </test>
26 <test> 33 <test>
27 <expand macro="test_input" /> 34 <expand macro="test_input" />
28 <param name="precalled" value="true" /> 35 <param name="precalled" value="true" />
29 <output name="output" file="poretools-events-out2.tabular" ftype="tabular" /> 36 <output name="output" ftype="tabular">
37 <assert_contents>
38 <has_n_lines n="3083"/>
39 <not_has_text text="template"/>
40 <not_has_text text="complement"/>
41 <has_text text="pre_basecalled"/>
42 </assert_contents>
43 </output>
30 </test> 44 </test>
31 </tests> 45 </tests>
32 <help> 46 <help>
33 Extract the raw nanopore events from each FAST5 file. 47 Extract the raw nanopore events from each FAST5 file.
34 </help> 48 </help>