annotate macros.xml @ 1:ea77d69db382 draft

"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 2df36b6d30fd69ea532a4fd42daf4741363074f3"
author iuc
date Sun, 28 Jun 2020 14:51:05 -0400
parents ceec541f4955
children 435344af6dc9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
2 <macros>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
3 <token name="@TOOL_VERSION@">3.1.3</token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
4 <token name="@TOOL_NAME@">ont_fast5_api:</token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
5 <xml name="requirements">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
6 <requirements>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
8 <requirement type="package" version="1.10.5">hdf5</requirement>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
9 </requirements>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
10 </xml>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
11
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
12 <!-- command -->
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
13 <token name="@BATCHSIZE@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
14 --batch_size $batch_size
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
15 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
16 <token name="@COMPRESSION@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
17 #if $compression != 'none'
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
18 --compression '$compression'
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
19 #end if
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
20 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
21 <token name="@INITIALIZE@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
22 mkdir -p './data' &&
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
23 tar -xf '$input_path' -C './data' &&
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
24 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
25 <token name="@INPUTPATH@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
26 --input_path './data'
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
27 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
28 <token name="@SAVEPATH@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
29 --save_path './results'
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
30 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
31 <token name="@TARBALL@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
32 && find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
33 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
34 <token name="@THREADS@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
35 --threads \${GALAXY_SLOTS:-4}
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
36 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
37
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
38 <!-- input -->
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
39 <xml name="input" token_argument="--input_path" token_label="multi">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
40 <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
41 </xml>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
42 <xml name="batch_size">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
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"/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
44 </xml>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
45 <xml name="compression">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
46 <param argument="compression" type="select" label="Select output compression type">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
47 <yield/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
48 <option value="vbz_legacy_v0">VBZ legacy v0</option>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
49 <option value="gzip">GZIP</option>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
50 </param>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
51 </xml>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
52
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
53 <!-- output -->
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
54 <xml name="output">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
55 <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results"/>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
56 </xml>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
57
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
58 <!-- help -->
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
59 <token name="@WID@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
60 *ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
61
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
62 - concrete implementation of the FAST5 file schema using the generic h5py library
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
63 - plain-english-named methods to interact with and reflect the FAST5 file schema
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
64 - tools to convert between multi_read and single_read formats
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
65 - tools to compress/decompress raw data in files
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
66 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
67 <token name="@REFERENCES@"><![CDATA[
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
68 More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_.
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
69 ]]></token>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
70
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
71 <xml name="citations">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
72 <citations>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
73 <citation type="bibtex">
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
74 @online{ont_fast5_api,
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
75 author = {Oxford Nanopore Technologies },
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
76 title = {ont_fast5_api},
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
77 year = 2020,
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
78 url = {https://github.com/nanoporetech/ont_fast5_api},
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
79 urldate = {2020-06-01}
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
80 }</citation>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
81 </citations>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
82 </xml>
ceec541f4955 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff changeset
83 </macros>