annotate tarfast5.xml @ 2:e660e8605dd8 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
author artbio
date Sun, 16 May 2021 18:20:09 +0000
parents 436f11e1ed6d
children 75ae798e310b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
1 <tool id="tarfast5" name="tarfast5" version="0.5.2">
0
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
2 <description></description>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
3 <requirements>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
4 <requirement type="package" version="2.6">pigz</requirement>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
5 <requirement type="package" version="1.34">tar</requirement>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
6 </requirements>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
7 <stdio>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
8 <exit_code range="1:" level="fatal" description="Tool exception" />
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
9 </stdio>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
11 #for $file in $inputs:
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
12 ln -s $file ${file.element_identifier}.h5 &&
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
13 #end for
2
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
14 #if $output_format == "gzip":
1
436f11e1ed6d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 8bd895c48953189b94dbe095db8767b82187a491"
artbio
parents: 0
diff changeset
15 export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
2
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
16 tar -cvh --use-compress-program=pigz -f $output *.h5
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
17 #else:
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
18 tar -cvh -f $output *.h5
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
19 #end if
0
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
20 ]]></command>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
21 <inputs>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
22 <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" />
2
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
23 <param name="output_format" type="select" label="compression of the tar archive" display="radio">
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
24 <option value="tar">tar (no compression)</option>
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
25 <option value="gzip" selected="true">tar.gz</option>
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
26 </param>
0
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
27 </inputs>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
28
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
29 <outputs>
2
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
30 <data format="fast5.tar" name="output" label="Archive of fast5" >
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
31 <change_format>
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
32 <when input="output_format" value="gzip" format="fast5.tar.gz"/>
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
33 </change_format>
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
34 </data>
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
35
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
36
0
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
37 </outputs>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
38
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
39 <tests>
2
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
40 <test> <!-- tar -->
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
41 <param name="inputs" value="F1.fast5.h5" ftype="h5" />
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
42 <param name="output_format" value="tar" />
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
43 <output file="archive.tar" name="output" compare="sim_size" delta="3000" />
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
44 </test>
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
45
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
46 <test> <!-- tar.gz -->
0
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
47 <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" />
2
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
48 <param name="output_format" value="gzip" />
e660e8605dd8 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 62909f7108d2d371e6461a4e3f8040ebb54f1ec0"
artbio
parents: 1
diff changeset
49 <output file="archive.tar.gz" name="output" compare="sim_size" delta="3000" />
0
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
50 </test>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
51 </tests>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
52 <help>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
53
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
54 **What it does**
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
55
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
56 Creates a tar.gz archive of fast5 (h5) sequences files
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
57
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
58 .. class:: warningmark
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
59
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
60 This tools follows a "map-reduce" procedure: multiple inputs, that can be arranged as a data collection,
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
61 are compressed into a single tar.gz archive.
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
62
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
63
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
64
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
65 **Output**
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
66
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
67 A fast5.tar.gz archive
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
68
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
69 </help>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
70
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
71 <citations>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
72 <citation type="doi">10.1093/bioinformatics/btp352</citation>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
73 <citation type="bibtex">@Book{,
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
74 title = {Lattice: Multivariate Data Visualization with R},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
75 author = {Deepayan Sarkar},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
76 publisher = {Springer},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
77 address = {New York},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
78 year = {2008},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
79 note = {ISBN 978-0-387-75968-5},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
80 url = {http://lmdvr.r-forge.r-project.org},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
81 }</citation>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
82 </citations>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
83 </tool>