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comparison gzip.xml @ 1:32b19379cd25 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
author artbio
date Wed, 06 Apr 2022 10:12:12 +0000
parents 401afd3c5220
children 285d48249ba2
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0:401afd3c5220 1:32b19379cd25
1 <tool id="justgzip" name="Gzip sequence datasets" version="0.1.0"> 1 <tool id="justgzip" name="Gzip datasets" version="0.2" profile="21.01">
2 <description></description> 2 <description></description>
3 <stdio> 3 <stdio>
4 <exit_code range="1:" level="fatal" description="Tool exception" /> 4 <exit_code range="1:" level="fatal" description="Tool exception" />
5 </stdio> 5 </stdio>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 gzip -ck '${input1}' > $output 7 gzip -c '${input1}' > '$output'
8 #if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]:
9 #set ext = $input1.ext + ".gz"
10 #else
11 #set ext = "gz"
12 #end if
13 && echo '{"output": {"ext": "$ext"}}' >> galaxy.json
8 ]]></command> 14 ]]></command>
9 <inputs> 15 <inputs>
10 <param format="fastq" name="input1" type="data" label="Input file" help="file to compress" /> 16 <param format="data" name="input1" type="data" label="Input file" help="file to compress" />
11 <param name="datatype" type="select" label="Input file datatype" help="Input file datatype" >
12 <option value="sanger" >fastqsanger </option>
13 <option value="illumina" >fastqillumina </option>
14 <option value="fastq" selected="true" >fastq </option>
15 </param>
16 </inputs> 17 </inputs>
17 <outputs> 18 <outputs>
18 19 <data name="output" format="auto" label="${input1.name}.gz" />
19 <data name="output" format="fastq.gz" label="$input1.name " >
20 <change_format>
21 <when input="datatype" value="sanger" format="fastqsanger.gz" />
22 <when input="datatype" value="illumina" format="fastqillumina.gz" />
23 </change_format>
24 </data>
25 </outputs> 20 </outputs>
26 <tests> 21 <tests>
27 <test> 22 <test>
28 <param name="input1" value="file1" ftype="fastq" /> 23 <param name="input1" value="file1" ftype="fastq" />
29 <param name="datatype" value="fastq" />
30 <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/> 24 <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/>
31 </test> 25 </test>
32 <test> 26 <test>
33 <param name="input1" value="file1" ftype="fastqsanger" /> 27 <param name="input1" value="file1" ftype="fastqsanger" />
34 <param name="datatype" value="sanger" />
35 <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" /> 28 <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" />
36 </test> 29 </test>
37 30
38 </tests> 31 </tests>
39 <help> 32 <help>
40 33
41 .. class:: infomark 34 .. class:: infomark
42 35
43 **What it does** 36 **What it does**
44 37
45 Just **gzip** fastq, fastqillumina and fastqsanger datasets. 38 Just **gzip** datasets.
46 39
47 </help> 40 </help>
48 </tool> 41 </tool>
49 42