Mercurial > repos > artbio > tarfast5
comparison tarfast5.xml @ 0:0e548765d204 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5 commit c06adf86d450d8c8965798ee60714fbcd41c90e3"
| author | artbio |
|---|---|
| date | Wed, 05 May 2021 00:22:41 +0000 |
| parents | |
| children | 436f11e1ed6d |
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| -1:000000000000 | 0:0e548765d204 |
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| 1 <tool id="tarfast5" name="tarfast5" version="0.3"> | |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.6">pigz</requirement> | |
| 5 <requirement type="package" version="1.34">tar</requirement> | |
| 6 </requirements> | |
| 7 <stdio> | |
| 8 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 9 </stdio> | |
| 10 <command detect_errors="exit_code"><![CDATA[ | |
| 11 #for $file in $inputs: | |
| 12 ln -s $file ${file.element_identifier}.h5 && | |
| 13 #end for | |
| 14 tar -I pigz -cvhf $compressed_output *.h5 | |
| 15 ]]></command> | |
| 16 <inputs> | |
| 17 <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" /> | |
| 18 </inputs> | |
| 19 | |
| 20 <outputs> | |
| 21 <data format="fast5.tar.gz" name="compressed_output" label="tar.gz archive of fast5" /> | |
| 22 </outputs> | |
| 23 | |
| 24 <tests> | |
| 25 <test> <!-- 0 --> | |
| 26 <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" /> | |
| 27 <output file="archive.tar.gz" name="compressed_output" compare="sim_size" delta="3000" /> | |
| 28 </test> | |
| 29 </tests> | |
| 30 <help> | |
| 31 | |
| 32 **What it does** | |
| 33 | |
| 34 Creates a tar.gz archive of fast5 (h5) sequences files | |
| 35 | |
| 36 .. class:: warningmark | |
| 37 | |
| 38 This tools follows a "map-reduce" procedure: multiple inputs, that can be arranged as a data collection, | |
| 39 are compressed into a single tar.gz archive. | |
| 40 | |
| 41 | |
| 42 | |
| 43 **Output** | |
| 44 | |
| 45 A fast5.tar.gz archive | |
| 46 | |
| 47 </help> | |
| 48 | |
| 49 <citations> | |
| 50 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
| 51 <citation type="bibtex">@Book{, | |
| 52 title = {Lattice: Multivariate Data Visualization with R}, | |
| 53 author = {Deepayan Sarkar}, | |
| 54 publisher = {Springer}, | |
| 55 address = {New York}, | |
| 56 year = {2008}, | |
| 57 note = {ISBN 978-0-387-75968-5}, | |
| 58 url = {http://lmdvr.r-forge.r-project.org}, | |
| 59 }</citation> | |
| 60 </citations> | |
| 61 </tool> |