Mercurial > repos > artbio > ont_fast5_api

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:0fbeff566070
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 '$input_path' -C './data' &&
24 ]]></token>
25 <token name="@INPUTPATH@"><![CDATA[
26 --input_path './data'
27 ]]></token>
28 <token name="@SAVEPATH@"><![CDATA[
29 --save_path './results'
30 ]]></token>
31 <token name="@TARBALL@"><![CDATA[
32 && find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin
33 ]]></token>
34 <token name="@THREADS@"><![CDATA[
35 --threads \${GALAXY_SLOTS:-4}
36 ]]></token>
37
38 <!-- input -->
39 <xml name="input" token_argument="--input_path" token_label="multi">
40 <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/>
41 </xml>
42 <xml name="batch_size">
43 <param argument="--batch_size" type="integer" value="4000" min="1" label="Set batch size" help="Number of single reads to include in each multi read file"/>
44 </xml>
45 <xml name="compression">
46 <param argument="compression" type="select" label="Select output compression type">
47 <option value="none" selected="true">None</option>
48 <option value="gzip">GZIP</option>
49 <option value="vbz_legacy_v0">VBZ legacy v0</option>
50 <option value="vbz">VBZ</option>
51 </param>
52 </xml>
53
54 <!-- output -->
55 <xml name="output">
56 <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results">
57 <change_format>
58 <when input="compression" value="gzip" format="fast5.tar.gz"/>
59 <when input="compression" value="vbz_legacy_v0" format="fast5.tar.bz2"/>
60 <when input="compression" value="vbz" format="fast5.tar.bz2"/>
61 </change_format>
62 </data>
63 <data name="summary" format="txt" from_work_dir="./results/*.txt" label="filename_mapping.txt" />
64 </xml>
65
66 <!-- help -->
67 <token name="@WID@"><![CDATA[
68 *ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.
69
70 - concrete implementation of the FAST5 file schema using the generic h5py library
71 - plain-english-named methods to interact with and reflect the FAST5 file schema
72 - tools to convert between multi_read and single_read formats
73 - tools to compress/decompress raw data in files
74 ]]></token>
75 <token name="@REFERENCES@"><![CDATA[
76 More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_.
77 ]]></token>
78
79 <xml name="citations">
80 <citations>
81 <citation type="bibtex">
82 @online{ont_fast5_api,
83 author = {Oxford Nanopore Technologies },
84 title = {ont_fast5_api},
85 year = 2020,
86 url = {https://github.com/nanoporetech/ont_fast5_api},
87 urldate = {2020-06-01}
88 }</citation>
89 </citations>
90 </xml>
91 </macros>