Mercurial > repos > iuc > ont_fast5_api_fast5_subset
comparison macros.xml @ 1:3bdd8fa109b1 draft
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
author | iuc |
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date | Fri, 12 Jun 2020 15:08:23 -0400 |
parents | eb1f4aa80c72 |
children | 0defe443ea04 |
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0:eb1f4aa80c72 | 1:3bdd8fa109b1 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 <token name="@TOOL_VERSION@">3.1.3</token> | 3 <token name="@TOOL_VERSION@">3.1.3</token> |
4 <token name="@TOOL_NAME@">ont_fast5_api:</token> | |
4 <xml name="requirements"> | 5 <xml name="requirements"> |
5 <requirements> | 6 <requirements> |
6 <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement> | 7 <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement> |
8 <requirement type="package" version="1.10.5">hdf5</requirement> | |
7 </requirements> | 9 </requirements> |
8 </xml> | 10 </xml> |
9 <xml name="citations"> | 11 |
10 <citations> | 12 <!-- command --> |
11 <citation type="bibtex">@online{ont_fast5_api, | 13 <token name="@BATCHSIZE@"><![CDATA[ |
12 author = {Oxford Nanopore Technologies }, | 14 --batch_size $batch_size |
13 title = {ont_fast5_api}, | 15 ]]></token> |
14 year = 2020, | 16 <token name="@COMPRESSION@"><![CDATA[ |
15 url = {https://github.com/nanoporetech/ont_fast5_api}, | 17 #if $compression != 'none' |
16 urldate = {2020-06-01} | 18 --compression '$compression' |
17 }</citation> | 19 #end if |
18 </citations> | 20 ]]></token> |
21 <token name="@INITIALIZE@"><![CDATA[ | |
22 mkdir -p './data' && | |
23 tar -xf '$input_path' -C './data' && | |
24 ]]></token> | |
25 <token name="@INPUTPATH@"><![CDATA[ | |
26 --input_path './data' | |
27 ]]></token> | |
28 <token name="@SAVEPATH@"><![CDATA[ | |
29 --save_path './results' | |
30 ]]></token> | |
31 <token name="@TARBALL@"><![CDATA[ | |
32 && find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin | |
33 ]]></token> | |
34 <token name="@THREADS@"><![CDATA[ | |
35 --threads \${GALAXY_SLOTS:-4} | |
36 ]]></token> | |
37 | |
38 <!-- input --> | |
39 <xml name="input" token_argument="--input_path" token_label="multi"> | |
40 <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/> | |
19 </xml> | 41 </xml> |
42 <xml name="batch_size"> | |
43 <param argument="--batch_size" type="integer" value="4000" min="1" label="Set batch size" help="Number of single reads to include in each multi read file"/> | |
44 </xml> | |
45 <xml name="compression"> | |
46 <param argument="compression" type="select" label="Select output compression type"> | |
47 <yield/> | |
48 <option value="vbz_legacy_v0">VBZ legacy v0</option> | |
49 <option value="gzip">GZIP</option> | |
50 </param> | |
51 </xml> | |
52 | |
53 <!-- output --> | |
54 <xml name="output"> | |
55 <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results"/> | |
56 </xml> | |
57 | |
58 <!-- help --> | |
20 <token name="@WID@"><![CDATA[ | 59 <token name="@WID@"><![CDATA[ |
21 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. | 60 *ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. |
22 | 61 |
23 - Concrete implementation of the FAST5 file schema using the generic h5py library | 62 - concrete implementation of the FAST5 file schema using the generic h5py library |
24 - Plain-english-named methods to interact with and reflect the FAST5 file schema | 63 - plain-english-named methods to interact with and reflect the FAST5 file schema |
25 - Tools to convert between multi_read and single_read formats | 64 - tools to convert between multi_read and single_read formats |
26 - Tools to compress/decompress raw data in files | 65 - tools to compress/decompress raw data in files |
27 ]]></token> | 66 ]]></token> |
28 <token name="@REFERENCES@"><![CDATA[ | 67 <token name="@REFERENCES@"><![CDATA[ |
29 More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_. | 68 More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_. |
30 ]]></token> | 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> | |
31 </macros> | 83 </macros> |