Mercurial > repos > artbio > ont_fast5_api

comparison fast5_subset.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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-1:000000000000 0:0fbeff566070
1 <?xml version="1.0"?>
2 <tool id="ont_fast5_api_fast5_subset" name="@TOOL_NAME@ Subset" version="@TOOL_VERSION@+galaxy2" profile="18.01">
3 <description>of multi read file(s)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <!-- no specific version command for subcommand fast5_subset available -->
9 <version_command><![CDATA[compress_fast5 -v]]></version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 ## initialize
12 mkdir -p './data' &&
13 tar -xf '$input' -C './data' &&
14
15 ## run
16 fast5_subset
17 --recursive
18 ## required
19 --input './data'
20 @SAVEPATH@
21 --read_id_list '$read_id_list'
22 ## optional
23 @COMPRESSION@
24 @BATCHSIZE@
25 @THREADS@
26
27 ## create tarball
28 @TARBALL@
29 ]]></command>
30 <inputs>
31 <expand macro="input" argument="--input"/>
32 <param argument="--read_id_list" type="data" format="txt,tabular" label="Select file with read IDs" help="Either containing 1 read_id per line or a tabular file with a column named read_id."/>
33 <expand macro="batch_size"/>
34 <expand macro="compression"/>
35 </inputs>
36 <outputs>
37 <expand macro="output"/>
38 </outputs>
39 <tests>
40 <!-- #1 default -->
41 <test expect_num_outputs="2">
42 <param name="input" value="multi.fast5.tar"/>
43 <param name="read_id_list" value="list.txt"/>
44 <output name="out_results">
45 <assert_contents>
46 <has_size value="30720"/>
47 </assert_contents>
48 </output>
49 <output name="summary" ftype="txt" value="filename_mapping_1.txt" compare="sim_size" delta="1" />
50 </test>
51 <!-- #2 -->
52 <test expect_num_outputs="2">
53 <param name="input" value="multi.fast5.tar"/>
54 <param name="read_id_list" value="list.txt"/>
55 <param name="batch_size" value="2"/>
56 <param name="compression" value="gzip"/>
57 <output name="out_results">
58 <assert_contents>
59 <has_size value="51200"/>
60 </assert_contents>
61 </output>
62 <output name="summary" ftype="txt" value="filename_mapping_2.txt" compare="sim_size" delta="1" />
63 </test>
64 <!-- #3 -->
65 <test expect_num_outputs="2">
66 <param name="input" value="multi.fast5.tar"/>
67 <param name="read_id_list" value="list.txt"/>
68 <param name="compression" value="vbz"/>
69 <output name="out_results">
70 <assert_contents>
71 <has_size value="40960"/>
72 </assert_contents>
73 </output>
74 </test>
75 <!-- #4 -->
76 <test expect_num_outputs="2">
77 <param name="input" value="multi.fast5.tar"/>
78 <param name="read_id_list" value="list.txt"/>
79 <param name="compression" value="vbz_legacy_v0"/>
80 <output name="out_results">
81 <assert_contents>
82 <has_size value="40960"/>
83 </assert_contents>
84 </output>
85 <output name="summary" ftype="txt" value="filename_mapping_4.txt" compare="sim_size" delta="1" />
86 </test>
87 </tests>
88 <help><![CDATA[
89 .. class:: infomark
90
91 **What it does**
92
93 @WID@
94
95 *fast5_subset* extracts reads from multi read FAST5 file(s) based on a list of read IDs.
96
97 **Input**
98
99 Multi read file(s) in FAST5 format, that are stored in a flat TAR, and a list of read IDs that should be extracted.
100
101 **Output**
102
103 Multi read file(s) in FAST5 format containing a subset of the input file(s). The rseults are are stored in a flat TAR.
104
105 .. class:: infomark
106
107 **References**
108
109 @REFERENCES@
110 ]]></help>
111 <expand macro="citations"/>
112 </tool>