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comparison compress_fast5.xml @ 0:0fbeff566070 draft default tip

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"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/ont_fast5_api commit 9fb27995131a4106053eb85d687857d2cbd2a5c6"
author artbio
date Sat, 22 May 2021 15:11:43 +0000
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1 <?xml version="1.0"?>
2 <tool id="ont_fast5_api_compress_fast5" name="@TOOL_NAME@ Compress" version="@TOOL_VERSION@+galaxy0" profile="18.01">
3 <description>multi read file(s)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <version_command><![CDATA[compress_fast5 -v]]></version_command>
9 <command detect_errors="exit_code"><![CDATA[
10 ## initialize
11 @INITIALIZE@
12
13 ## run
14 compress_fast5
15 --recursive
16 ## required
17 @INPUTPATH@
18 @SAVEPATH@
19 --compression '$compression'
20 ## optional
21 @THREADS@
22
23 ## create tarball
24 @TARBALL@
25 ]]></command>
26 <inputs>
27 <expand macro="input"/>
28 <param argument="compression" type="select" label="Select output compression type">
29 <option value="gzip" selected="true">GZIP</option>
30 <option value="vbz_legacy_v0">VBZ legacy v0</option>
31 <option value="vbz">VBZ</option>
32 </param>
33 </inputs>
34 <outputs>
35 <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results">
36 <change_format>
37 <when input="compression" value="gzip" format="fast5.tar.gz"/>
38 <when input="compression" value="vbz_legacy_v0" format="fast5.tar.bz2"/>
39 <when input="compression" value="vbz" format="fast5.tar.bz2"/>
40 </change_format>
41 </data>
42 </outputs>
43 <tests>
44 <!-- #1 default -->
45 <test expect_num_outputs="1">
46 <param name="input_path" value="multi.fast5.tar"/>
47 <param name="compression" value="vbz"/>
48 <output name="out_results">
49 <assert_contents>
50 <has_size value="40960"/>
51 </assert_contents>
52 </output>
53 </test>
54 <!-- #2 -->
55 <test expect_num_outputs="1">
56 <param name="input_path" value="multi.fast5.tar"/>
57 <param name="compression" value="vbz_legacy_v0"/>
58 <output name="out_results">
59 <assert_contents>
60 <has_size value="40960"/>
61 </assert_contents>
62 </output>
63 </test>
64 <!-- #3 -->
65 <test expect_num_outputs="1">
66 <param name="input_path" value="multi.fast5.tar"/>
67 <param name="compression" value="gzip"/>
68 <output name="out_results">
69 <assert_contents>
70 <has_size value="40960"/>
71 </assert_contents>
72 </output>
73 </test>
74 </tests>
75 <help><![CDATA[
76 .. class:: infomark
77
78 **What it does**
79
80 @WID@
81
82 *compress_fast5* copies and converts raw data between vbz and gzip compression formats.
83
84 **Input**
85
86 Multi read file(s) in FAST5 format that are stored in a flat TAR.
87
88 **Output**
89
90 Multi read FAST5 file(s) containing compressed reads that are stored in a flat TAR. Further detail of HDF5 data management strategies can be found `here <https://support.hdfgroup.org/HDF5/doc/Advanced/FileSpaceManagement/FileSpaceManagement.pdf>`_.
91
92 .. class:: infomark
93
94 **References**
95
96 @REFERENCES@
97 ]]></help>
98 <expand macro="citations"/>
99 </tool>