Mercurial > repos > artbio > tarfast5
changeset 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 |
| files | tarfast5.xml test-data/F1.fast5.h5 test-data/F2.fast5.h5 test-data/archive.tar.gz |
| diffstat | 4 files changed, 61 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tarfast5.xml Wed May 05 00:22:41 2021 +0000 @@ -0,0 +1,61 @@ +<tool id="tarfast5" name="tarfast5" version="0.3"> + <description></description> + <requirements> + <requirement type="package" version="2.6">pigz</requirement> + <requirement type="package" version="1.34">tar</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + #for $file in $inputs: + ln -s $file ${file.element_identifier}.h5 && + #end for + tar -I pigz -cvhf $compressed_output *.h5 + ]]></command> + <inputs> + <param name="inputs" type="data" format="h5" label="fast5 sequence files" multiple="true" /> + </inputs> + + <outputs> + <data format="fast5.tar.gz" name="compressed_output" label="tar.gz archive of fast5" /> +</outputs> + + <tests> + <test> <!-- 0 --> + <param name="inputs" value="F1.fast5.h5,F2.fast5.h5" ftype="h5" /> + <output file="archive.tar.gz" name="compressed_output" compare="sim_size" delta="3000" /> + </test> + </tests> +<help> + +**What it does** + +Creates a tar.gz archive of fast5 (h5) sequences files + +.. class:: warningmark + +This tools follows a "map-reduce" procedure: multiple inputs, that can be arranged as a data collection, +are compressed into a single tar.gz archive. + + + +**Output** + +A fast5.tar.gz archive + +</help> + +<citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="bibtex">@Book{, + title = {Lattice: Multivariate Data Visualization with R}, + author = {Deepayan Sarkar}, + publisher = {Springer}, + address = {New York}, + year = {2008}, + note = {ISBN 978-0-387-75968-5}, + url = {http://lmdvr.r-forge.r-project.org}, + }</citation> +</citations> +</tool>