Mercurial > repos > iuc > ont_fast5_api_multi_to_single_fast5

comparison macros.xml @ 0:8fdd2eaf95e2 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 19:05:31 +0000
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children eb214aad4e39
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-1:000000000000 0:8fdd2eaf95e2
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">3.1.3</token>
4 <token name="@TOOL_NAME@">ont_fast5_api:</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement>
8 <requirement type="package" version="1.10.5">hdf5</requirement>
9 </requirements>
10 </xml>
11
12 <!-- command -->
13 <token name="@BATCHSIZE@"><![CDATA[
14 --batch_size $batch_size
15 ]]></token>
16 <token name="@COMPRESSION@"><![CDATA[
17 #if $compression != 'none'
18 --compression '$compression'
19 #end if
20 ]]></token>
21 <token name="@INITIALIZE@"><![CDATA[
22 mkdir -p './data' &&
23 tar -xf '$input_path' -C './data' &&
24 ]]></token>
25 <token name="@INPUTPATH@"><![CDATA[
26 --input_path './data'
27 ]]></token>
28 <token name="@SAVEPATH@"><![CDATA[
29 --save_path './results'
30 ]]></token>
31 <token name="@TARBALL@"><![CDATA[
32 && find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin
33 ]]></token>
34 <token name="@THREADS@"><![CDATA[
35 --threads \${GALAXY_SLOTS:-4}
36 ]]></token>
37
38 <!-- input -->
39 <xml name="input" token_argument="--input_path" token_label="multi">
40 <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/>
41 </xml>
42 <xml name="batch_size">
43 <param argument="--batch_size" type="integer" value="4000" min="1" label="Set batch size" help="Number of single reads to include in each multi read file"/>
44 </xml>
45 <xml name="compression">
46 <param argument="compression" type="select" label="Select output compression type">
47 <yield/>
48 <option value="vbz_legacy_v0">VBZ legacy v0</option>
49 <option value="gzip">GZIP</option>
50 </param>
51 </xml>
52
53 <!-- output -->
54 <xml name="output">
55 <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results"/>
56 </xml>
57
58 <!-- help -->
59 <token name="@WID@"><![CDATA[
60 *ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.
61
62 - concrete implementation of the FAST5 file schema using the generic h5py library
63 - plain-english-named methods to interact with and reflect the FAST5 file schema
64 - tools to convert between multi_read and single_read formats
65 - tools to compress/decompress raw data in files
66 ]]></token>
67 <token name="@REFERENCES@"><![CDATA[
68 More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_.
69 ]]></token>
70
71 <xml name="citations">
72 <citations>
73 <citation type="bibtex">
74 @online{ont_fast5_api,
75 author = {Oxford Nanopore Technologies },
76 title = {ont_fast5_api},
77 year = 2020,
78 url = {https://github.com/nanoporetech/ont_fast5_api},
79 urldate = {2020-06-01}
80 }</citation>
81 </citations>
82 </xml>
83 </macros>