Mercurial > repos > artbio > justgzip

annotate gzip.xml @ 0:401afd3c5220 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children 32b19379cd25
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
1 <tool id="justgzip" name="Gzip sequence datasets" version="0.1.0">
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
2 <description></description>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
3 <stdio>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
4 <exit_code range="1:" level="fatal" description="Tool exception" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
5 </stdio>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
7 gzip -ck '${input1}' > $output
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
8 ]]></command>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
9 <inputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
10 <param format="fastq" name="input1" type="data" label="Input file" help="file to compress" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
11 <param name="datatype" type="select" label="Input file datatype" help="Input file datatype" >
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
12 <option value="sanger" >fastqsanger </option>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
13 <option value="illumina" >fastqillumina </option>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
14 <option value="fastq" selected="true" >fastq </option>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
15 </param>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
16 </inputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
17 <outputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
18
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
19 <data name="output" format="fastq.gz" label="$input1.name " >
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
20 <change_format>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
21 <when input="datatype" value="sanger" format="fastqsanger.gz" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
22 <when input="datatype" value="illumina" format="fastqillumina.gz" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
23 </change_format>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
24 </data>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
25 </outputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
26 <tests>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
27 <test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
28 <param name="input1" value="file1" ftype="fastq" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
29 <param name="datatype" value="fastq" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
30 <output name="output" file="file1.gz" decompress="True" ftype="fastq.gz"/>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
31 </test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
32 <test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
33 <param name="input1" value="file1" ftype="fastqsanger" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
34 <param name="datatype" value="sanger" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
35 <output name="output" file="file1.gz" decompress="True" ftype="fastqsanger.gz" />
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
36 </test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
37
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
38 </tests>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
39 <help>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
40
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
41 .. class:: infomark
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
42
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
43 **What it does**
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
44
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
45 Just **gzip** fastq, fastqillumina and fastqsanger datasets.
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
46
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
47 </help>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
48 </tool>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
49