Mercurial > repos > artbio > justgzip

annotate gzip.xml @ 1:32b19379cd25 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 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
author artbio
date Wed, 06 Apr 2022 10:12:12 +0000
parents 401afd3c5220
children 285d48249ba2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
1 <tool id="justgzip" name="Gzip datasets" version="0.2" profile="21.01">
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[
1
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
7 gzip -c '${input1}' > '$output'
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
8 #if ($input1.ext.startswith("fastq") and not $input1.ext.endswith(".gz")) or $input1.ext in ["fasta", "paf", "gff3", "nii1", "nii2", "gii", "tabular"]:
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
9 #set ext = $input1.ext + ".gz"
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
10 #else
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
11 #set ext = "gz"
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
12 #end if
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
13 && echo '{"output": {"ext": "$ext"}}' >> galaxy.json
0
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
14 ]]></command>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
15 <inputs>
1
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
16 <param format="data" name="input1" type="data" label="Input file" help="file to compress" />
0
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
17 </inputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
18 <outputs>
1
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
19 <data name="output" format="auto" label="${input1.name}.gz" />
0
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
20 </outputs>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
21 <tests>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
22 <test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
23 <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
24 <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
25 </test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
26 <test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
27 <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
28 <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
29 </test>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
30
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
31 </tests>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
32 <help>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
33
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
34 .. class:: infomark
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
35
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
36 **What it does**
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
37
1
32b19379cd25 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit 33e1e0491fc6ba65ac9777c06a7f736592f6d2e3"
artbio
parents: 0
diff changeset
38 Just **gzip** datasets.
0
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
39
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
40 </help>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
41 </tool>
401afd3c5220 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/justgzip commit cb119427c41b729c90572c410f717282ad9cb8a7
artbio
parents:
diff changeset
42