Mercurial > repos > iuc > ont_fast5_api_single_to_multi_fast5

comparison single_to_multi_fast5.xml @ 0:ceec541f4955 draft

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"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
author iuc
date Fri, 12 Jun 2020 15:08:04 -0400
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children ea77d69db382
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-1:000000000000 0:ceec541f4955
1 <?xml version="1.0"?>
2 <tool id="ont_fast5_api_single_to_multi_fast5" name="@TOOL_NAME@ Single to multi" version="@TOOL_VERSION@+galaxy0" profile="18.01">
3 <description>read file(s)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <version_command><![CDATA[single_to_multi -v]]></version_command>
9 <command detect_errors="exit_code"><![CDATA[
10 ## initialize
11 @INITIALIZE@
12
13 ## run
14 single_to_multi_fast5
15 ## required
16 @INPUTPATH@
17 @SAVEPATH@
18 ## optional
19 @COMPRESSION@
20 @BATCHSIZE@
21 @THREADS@
22
23 ## create tarball
24 @TARBALL@
25 ]]></command>
26 <inputs>
27 <expand macro="input" label="single"/>
28 <expand macro="batch_size"/>
29 <expand macro="compression">
30 <option value="none" selected="true">None</option>
31 <option value="vbz">VBZ</option>
32 </expand>
33 </inputs>
34 <outputs>
35 <expand macro="output"/>
36 </outputs>
37 <tests>
38 <!-- #1 default -->
39 <test expect_num_outputs="1">
40 <param name="input_path" value="single.fast5.tar"/>
41 <output name="out_results">
42 <assert_contents>
43 <has_size value="40960"/>
44 </assert_contents>
45 </output>
46 </test>
47 <!-- #2 -->
48 <test expect_num_outputs="1">
49 <param name="input_path" value="single.fast5.tar"/>
50 <param name="batch_size" value="3"/>
51 <param name="compression" value="vbz"/>
52 <output name="out_results">
53 <assert_contents>
54 <has_size value="51200"/>
55 </assert_contents>
56 </output>
57 </test>
58 <!-- #3 -->
59 <test expect_num_outputs="1">
60 <param name="input_path" value="single.fast5.tar"/>
61 <param name="compression" value="vbz_legacy_v0"/>
62 <output name="out_results">
63 <assert_contents>
64 <has_size value="40960"/>
65 </assert_contents>
66 </output>
67 </test>
68 <!-- #4 -->
69 <test expect_num_outputs="1">
70 <param name="input_path" value="single.fast5.tar"/>
71 <param name="compression" value="gzip"/>
72 <output name="out_results">
73 <assert_contents>
74 <has_size value="40960"/>
75 </assert_contents>
76 </output>
77 </test>
78 </tests>
79 <help><![CDATA[
80 .. class:: infomark
81
82 **What it does**
83
84 @WID@
85
86 *single_to_multi_fast5* converts single read FAST5 files into multi read FAST5 file(s).
87
88 **Input**
89
90 Single read files in FAST5 format that are stored in a flat TAR.
91
92 **Output**
93
94 Multi read file(s) in FAST5 format that are stored in a flat TAR.
95
96 .. class:: infomark
97
98 **References**
99
100 @REFERENCES@
101 ]]></help>
102 <expand macro="citations"/>
103 </tool>