Mercurial > repos > imgteam > unzip

annotate unzip.xml @ 0:ec30427e0d42 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
author imgteam
date Thu, 01 Aug 2019 11:04:14 -0400
parents
children 38eec75fbe9b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
1 <tool id="unzip" name="Unzip" version="0.1">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
2 <description>Unzip file</description>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
3 <requirements>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
4 <requirement type="package">unzip</requirement>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
5 <requirement type="package">tar</requirement>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
6 </requirements>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
7 <command>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
8 <![CDATA[
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
9 mkdir ./out &&
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
10 #if $input_file.is_of_type("zip"):
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
11 unzip "$input_file"
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
12 #if $extract_options['extract_all'] == 'False'
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
13 "$extract_options['pathtofile']"
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
14 #end if
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
15 -d out/
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
16 #end if
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
17 #if $input_file.is_of_type("tar"):
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
18 tar -xf "$input_file"
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
19 #if $extract_options['extract_all'] == 'False'
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
20 "$extract_options['pathtofile']"
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
21 #end if
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
22 -C ./out/
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
23 #end if
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
24 ]]>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
25 </command>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
26 <inputs>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
27 <param label="input_file" name="input_file" type="data" format="zip,tar"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
28
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
29 <conditional name="extract_options">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
30 <param label="Extract single file" name="extract_all" type="select">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
31 <option selected="True" value="True">All files</option>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
32 <option value="False">Single file</option>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
33 </param>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
34 <when value="True"></when>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
35 <when value="False">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
36 <param name="pathtofile" type="text" value="" label="Filepath">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
37 <sanitizer invalid_char="">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
38 <valid initial="string.ascii_letters,string.digits">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
39 <add value="_" />
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
40 <add value="/" />
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
41 <add value="." />
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
42 <add value="/../" />
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
43 </valid>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
44 </sanitizer>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
45 </param>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
46 </when>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
47 </conditional>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
48 </inputs>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
49 <outputs>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
50 <data name="unzipped_single">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
51 <discover_datasets pattern="__name__" directory="out" visible="true" ext="data" assign_primary_output="true" />
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
52 <filter>extract_options['extract_all'] == 'False'</filter>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
53 </data>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
54 <collection name="unzipped" type="list" label="${tool.name} on ${on_string}">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
55 <discover_datasets pattern="__name__" ext="data" directory="out" visible="false"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
56 <filter>extract_options['extract_all'] == 'True'</filter>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
57 </collection>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
58 </outputs>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
59 <tests>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
60 <test>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
61 <param name="input_file" value="input.zip" ftype="zip"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
62 <param name="extract_all" value="False"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
63 <param name="pathtofile" value="input.png"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
64 <output name="unzipped_single" file="input.png" ftype="data" compare="sim_size" />
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
65 </test>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
66 <test>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
67 <param name="input_file" value="input.zip" ftype="zip"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
68 <param name="extract_all" value="True"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
69 <output_collection name="unzipped" type="list">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
70 <element name="input.png" file="input.png" ftype="data" compare="sim_size"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
71 <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
72 </output_collection>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
73 </test>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
74 <test>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
75 <param name="input_file" value="input.tar" ftype="tar"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
76 <param name="extract_all" value="True"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
77 <output_collection name="unzipped" type="list">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
78 <element name="input.png" file="input.png" ftype="data" compare="sim_size"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
79 <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
80 </output_collection>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
81 </test>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
82 </tests>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
83 <help>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
84 **What it does**
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
85
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
86 Unzip folder to collection.
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
87 </help>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
88 <citations>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
89 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
90 </citations>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
91 </tool>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
imgteam
parents:
diff changeset
92