Mercurial > repos > artbio > justgzip
changeset 2:285d48249ba2 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip commit d995baa7680d2a9e6b5ae8903cf7e5e29ae47d3d
| author | artbio |
|---|---|
| date | Wed, 13 Dec 2023 00:20:07 +0000 |
| parents | 32b19379cd25 |
| children | |
| files | gzip.xml test-data/file1.gz |
| diffstat | 2 files changed, 33 insertions(+), 14 deletions(-) [+] |
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--- a/gzip.xml Wed Apr 06 10:12:12 2022 +0000 +++ b/gzip.xml Wed Dec 13 00:20:07 2023 +0000 @@ -1,22 +1,28 @@ -<tool id="justgzip" name="Gzip datasets" version="0.2" profile="21.01"> +<tool id="justgzip" name="Gzip datasets" version="2.8+galaxy0" profile="21.01"> <description></description> + + <requirements> + <requirement type="package" version="2.8">pigz</requirement> + </requirements> + <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> - <command detect_errors="exit_code"><![CDATA[ -gzip -c '${input1}' > '$output' -#if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]: - #set ext = $input1.ext + ".gz" -#else - #set ext = "gz" -#end if -&& echo '{"output": {"ext": "$ext"}}' >> galaxy.json + + <command detect_errors="exit_code"><![CDATA[ + pigz --processes \${GALAXY_SLOTS:-4} -c '${input1}' > '$output' + #if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]: + #set ext = $input1.ext + ".gz" + #else + #set ext = "gz" + #end if + && echo '{"output": {"ext": "$ext"}}' >> galaxy.json ]]></command> <inputs> - <param format="data" name="input1" type="data" label="Input file" help="file to compress" /> + <param format="data" name="input1" type="data" label="Input file" help="file to compress" /> </inputs> <outputs> - <data name="output" format="auto" label="${input1.name}.gz" /> + <data name="output" format="auto" label="${input1.name}.gz" /> </outputs> <tests> <test> @@ -27,16 +33,29 @@ <param name="input1" value="file1" ftype="fastqsanger" /> <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" /> </test> + </tests> - </tests> <help> .. class:: infomark **What it does** -Just **gzip** datasets. - +Just **gzip** datasets, but does it faster with the multithreaded pigz program ! + + Accepted input formats include: + - fastq + - fastqsanger + - fasta + - paf + - gff3 + - nii1 + - nii2 + - gii + - tabular + - txt + - ... + </help> </tool>