Mercurial > repos > artbio > tarfast5

annotate tarfast5.xml @ 1:436f11e1ed6d draft

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/tarfast5 commit 8bd895c48953189b94dbe095db8767b82187a491"
author artbio
date Thu, 06 May 2021 23:12:50 +0000
parents 0e548765d204
children e660e8605dd8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
436f11e1ed6d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 8bd895c48953189b94dbe095db8767b82187a491"
artbio
parents: 0
diff changeset
1 <tool id="tarfast5" name="tarfast5" version="0.4">
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
1
436f11e1ed6d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 8bd895c48953189b94dbe095db8767b82187a491"
artbio
parents: 0
diff changeset
14 export PIGZ="-p \${GALAXY_SLOTS:-4}" &&
436f11e1ed6d "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit 8bd895c48953189b94dbe095db8767b82187a491"
artbio
parents: 0
diff changeset
15 tar -cvh --use-compress-program=pigz -f $compressed_output *.h5
0
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
16 ]]></command>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
17 <inputs>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
18 <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" />
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
19 </inputs>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
20
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
21 <outputs>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
22 <data format="fast5.tar.gz" name="compressed_output" label="tar.gz archive of fast5" />
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
23 </outputs>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
24
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
25 <tests>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
26 <test> <!-- 0 -->
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
27 <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" />
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
28 <output file="archive.tar.gz" name="compressed_output" compare="sim_size" delta="3000" />
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
29 </test>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
30 </tests>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
31 <help>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
32
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
33 **What it does**
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
34
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
35 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
36
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
37 .. class:: warningmark
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 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
40 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
41
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
42
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
43
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
44 **Output**
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
45
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
46 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
47
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
48 </help>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
49
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
50 <citations>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
51 <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
52 <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
53 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
54 author = {Deepayan Sarkar},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
55 publisher = {Springer},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
56 address = {New York},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
57 year = {2008},
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
58 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
59 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
60 }</citation>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
61 </citations>
0e548765d204 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
artbio
parents:
diff changeset
62 </tool>