Mercurial > repos > iuc > ont_fast5_api_single_to_multi_fast5
annotate single_to_multi_fast5.xml @ 0:ceec541f4955 draft
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
author | iuc |
---|---|
date | Fri, 12 Jun 2020 15:08:04 -0400 |
parents | |
children | ea77d69db382 |
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 <tool id="ont_fast5_api_single_to_multi_fast5" name="@TOOL_NAME@ Single to multi" version="@TOOL_VERSION@+galaxy0" profile="18.01"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
3 <description>read file(s)</description> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
4 <macros> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
5 <import>macros.xml</import> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
6 </macros> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
7 <expand macro="requirements"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
8 <version_command><![CDATA[single_to_multi -v]]></version_command> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
9 <command detect_errors="exit_code"><![CDATA[ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
10 ## initialize |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
11 @INITIALIZE@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
12 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
13 ## run |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
14 single_to_multi_fast5 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
15 ## required |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
16 @INPUTPATH@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
17 @SAVEPATH@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
18 ## optional |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
19 @COMPRESSION@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
20 @BATCHSIZE@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
21 @THREADS@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
22 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
23 ## create tarball |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
24 @TARBALL@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
25 ]]></command> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
26 <inputs> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
27 <expand macro="input" label="single"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
28 <expand macro="batch_size"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
29 <expand macro="compression"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
30 <option value="none" selected="true">None</option> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
31 <option value="vbz">VBZ</option> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
32 </expand> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
33 </inputs> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
34 <outputs> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
35 <expand macro="output"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
36 </outputs> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
37 <tests> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
38 <!-- #1 default --> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
39 <test expect_num_outputs="1"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
40 <param name="input_path" value="single.fast5.tar"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
41 <output name="out_results"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
42 <assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
43 <has_size value="40960"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
44 </assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
45 </output> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
46 </test> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
47 <!-- #2 --> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
48 <test expect_num_outputs="1"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
49 <param name="input_path" value="single.fast5.tar"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
50 <param name="batch_size" value="3"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
51 <param name="compression" value="vbz"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
52 <output name="out_results"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
53 <assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
54 <has_size value="51200"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
55 </assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
56 </output> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
57 </test> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
58 <!-- #3 --> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
59 <test expect_num_outputs="1"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
60 <param name="input_path" value="single.fast5.tar"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
61 <param name="compression" value="vbz_legacy_v0"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
62 <output name="out_results"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
63 <assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
64 <has_size value="40960"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
65 </assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
66 </output> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
67 </test> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
68 <!-- #4 --> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
69 <test expect_num_outputs="1"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
70 <param name="input_path" value="single.fast5.tar"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
71 <param name="compression" value="gzip"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
72 <output name="out_results"> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
73 <assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
74 <has_size value="40960"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
75 </assert_contents> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
76 </output> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
77 </test> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
78 </tests> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
79 <help><![CDATA[ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
80 .. class:: infomark |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
81 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
82 **What it does** |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
83 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
84 @WID@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
85 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
86 *single_to_multi_fast5* converts single read FAST5 files into multi read FAST5 file(s). |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
87 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
88 **Input** |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
89 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
90 Single read files in FAST5 format that are stored in a flat TAR. |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
91 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
92 **Output** |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
93 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
94 Multi read file(s) in FAST5 format that are stored in a flat TAR. |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
95 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
96 .. class:: infomark |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
97 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
98 **References** |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
99 |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
100 @REFERENCES@ |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
101 ]]></help> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
102 <expand macro="citations"/> |
ceec541f4955
"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"
iuc
parents:
diff
changeset
|
103 </tool> |