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comparison gzip.xml @ 0:401afd3c5220 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
author artbio
date Wed, 16 May 2018 12:59:10 -0400
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children 32b19379cd25
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-1:000000000000 0:401afd3c5220
1 <tool id="justgzip" name="Gzip sequence datasets" version="0.1.0">
2 <description></description>
3 <stdio>
4 <exit_code range="1:" level="fatal" description="Tool exception" />
5 </stdio>
6 <command detect_errors="exit_code"><![CDATA[
7 gzip -ck '${input1}' > $output
8 ]]></command>
9 <inputs>
10 <param format="fastq" name="input1" type="data" label="Input file" help="file to compress" />
11 <param name="datatype" type="select" label="Input file datatype" help="Input file datatype" >
12 <option value="sanger" >fastqsanger </option>
13 <option value="illumina" >fastqillumina </option>
14 <option value="fastq" selected="true" >fastq </option>
15 </param>
16 </inputs>
17 <outputs>
18
19 <data name="output" format="fastq.gz" label="$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>
26 <tests>
27 <test>
28 <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"/>
31 </test>
32 <test>
33 <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" />
36 </test>
37
38 </tests>
39 <help>
40
41 .. class:: infomark
42
43 **What it does**
44
45 Just **gzip** fastq, fastqillumina and fastqsanger datasets.
46
47 </help>
48 </tool>
49