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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
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1:32b19379cd25 2:285d48249ba2
1 <tool id="justgzip" name="Gzip datasets" version="0.2" profile="21.01"> 1 <tool id="justgzip" name="Gzip datasets" version="2.8+galaxy0" profile="21.01">
2 <description></description> 2 <description></description>
3
4 <requirements>
5 <requirement type="package" version="2.8">pigz</requirement>
6 </requirements>
7
3 <stdio> 8 <stdio>
4 <exit_code range="1:" level="fatal" description="Tool exception" /> 9 <exit_code range="1:" level="fatal" description="Tool exception" />
5 </stdio> 10 </stdio>
6 <command detect_errors="exit_code"><![CDATA[ 11
7 gzip -c '${input1}' > '$output' 12 <command detect_errors="exit_code"><![CDATA[
8 #if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]: 13 pigz --processes \${GALAXY_SLOTS:-4} -c '${input1}' > '$output'
9 #set ext = $input1.ext + ".gz" 14 #if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]:
10 #else 15 #set ext = $input1.ext + ".gz"
11 #set ext = "gz" 16 #else
12 #end if 17 #set ext = "gz"
13 && echo '{"output": {"ext": "$ext"}}' >> galaxy.json 18 #end if
19 && echo '{"output": {"ext": "$ext"}}' >> galaxy.json
14 ]]></command> 20 ]]></command>
15 <inputs> 21 <inputs>
16 <param format="data" name="input1" type="data" label="Input file" help="file to compress" /> 22 <param format="data" name="input1" type="data" label="Input file" help="file to compress" />
17 </inputs> 23 </inputs>
18 <outputs> 24 <outputs>
19 <data name="output" format="auto" label="${input1.name}.gz" /> 25 <data name="output" format="auto" label="${input1.name}.gz" />
20 </outputs> 26 </outputs>
21 <tests> 27 <tests>
22 <test> 28 <test>
23 <param name="input1" value="file1" ftype="fastq" /> 29 <param name="input1" value="file1" ftype="fastq" />
24 <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/> 30 <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/>
25 </test> 31 </test>
26 <test> 32 <test>
27 <param name="input1" value="file1" ftype="fastqsanger" /> 33 <param name="input1" value="file1" ftype="fastqsanger" />
28 <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" /> 34 <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" />
29 </test> 35 </test>
36 </tests>
30 37
31 </tests>
32 <help> 38 <help>
33 39
34 .. class:: infomark 40 .. class:: infomark
35 41
36 **What it does** 42 **What it does**
37 43
38 Just **gzip** datasets. 44 Just **gzip** datasets, but does it faster with the multithreaded pigz program !
39 45
46 Accepted input formats include:
47 - fastq
48 - fastqsanger
49 - fasta
50 - paf
51 - gff3
52 - nii1
53 - nii2
54 - gii
55 - tabular
56 - txt
57 - ...
58
40 </help> 59 </help>
41 </tool> 60 </tool>
42 61