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comparison unzip.xml @ 0:ec30427e0d42 draft

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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
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children 38eec75fbe9b
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-1:000000000000 0:ec30427e0d42
1 <tool id="unzip" name="Unzip" version="0.1">
2 <description>Unzip file</description>
3 <requirements>
4 <requirement type="package">unzip</requirement>
5 <requirement type="package">tar</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 mkdir ./out &&
10 #if $input_file.is_of_type("zip"):
11 unzip "$input_file"
12 #if $extract_options['extract_all'] == 'False'
13 "$extract_options['pathtofile']"
14 #end if
15 -d out/
16 #end if
17 #if $input_file.is_of_type("tar"):
18 tar -xf "$input_file"
19 #if $extract_options['extract_all'] == 'False'
20 "$extract_options['pathtofile']"
21 #end if
22 -C ./out/
23 #end if
24 ]]>
25 </command>
26 <inputs>
27 <param label="input_file" name="input_file" type="data" format="zip,tar"/>
28
29 <conditional name="extract_options">
30 <param label="Extract single file" name="extract_all" type="select">
31 <option selected="True" value="True">All files</option>
32 <option value="False">Single file</option>
33 </param>
34 <when value="True"></when>
35 <when value="False">
36 <param name="pathtofile" type="text" value="" label="Filepath">
37 <sanitizer invalid_char="">
38 <valid initial="string.ascii_letters,string.digits">
39 <add value="_" />
40 <add value="/" />
41 <add value="." />
42 <add value="/../" />
43 </valid>
44 </sanitizer>
45 </param>
46 </when>
47 </conditional>
48 </inputs>
49 <outputs>
50 <data name="unzipped_single">
51 <discover_datasets pattern="__name__" directory="out" visible="true" ext="data" assign_primary_output="true" />
52 <filter>extract_options['extract_all'] == 'False'</filter>
53 </data>
54 <collection name="unzipped" type="list" label="${tool.name} on ${on_string}">
55 <discover_datasets pattern="__name__" ext="data" directory="out" visible="false"/>
56 <filter>extract_options['extract_all'] == 'True'</filter>
57 </collection>
58 </outputs>
59 <tests>
60 <test>
61 <param name="input_file" value="input.zip" ftype="zip"/>
62 <param name="extract_all" value="False"/>
63 <param name="pathtofile" value="input.png"/>
64 <output name="unzipped_single" file="input.png" ftype="data" compare="sim_size" />
65 </test>
66 <test>
67 <param name="input_file" value="input.zip" ftype="zip"/>
68 <param name="extract_all" value="True"/>
69 <output_collection name="unzipped" type="list">
70 <element name="input.png" file="input.png" ftype="data" compare="sim_size"/>
71 <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/>
72 </output_collection>
73 </test>
74 <test>
75 <param name="input_file" value="input.tar" ftype="tar"/>
76 <param name="extract_all" value="True"/>
77 <output_collection name="unzipped" type="list">
78 <element name="input.png" file="input.png" ftype="data" compare="sim_size"/>
79 <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/>
80 </output_collection>
81 </test>
82 </tests>
83 <help>
84 **What it does**
85
86 Unzip folder to collection.
87 </help>
88 <citations>
89 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
90 </citations>
91 </tool>
92