Mercurial > repos > imgteam > unzip

comparison unzip.xml @ 1:38eec75fbe9b 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 ab38debe1175446664e9bede9be8c667894bf9f1
author imgteam
date Fri, 02 Aug 2019 07:21:01 -0400
parents ec30427e0d42
children 57f0914ddb7b
comparison
equal deleted inserted replaced
0:ec30427e0d42 1:38eec75fbe9b
1 <tool id="unzip" name="Unzip" version="0.1"> 1 <tool id="unzip" name="Unzip" version="0.2">
2 <description>Unzip file</description> 2 <description>Unzip file</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">unzip</requirement> 4 <requirement type="package">unzip</requirement>
5 <requirement type="package">tar</requirement> 5 <requirement type="package">tar</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 <![CDATA[ 8 <![CDATA[
9 mkdir ./out && 9 mkdir ./out &&
10 #if $input_file.is_of_type("zip"): 10 #if $input_file.is_of_type("zip"):
11 unzip "$input_file" 11 unzip
12 #if $extract_options['extract_all'] == 'False' 12 #if $extract_options['extract_all'] == 'False'
13 "$extract_options['pathtofile']" 13 -p "$input_file" "$extract_options['pathtofile']" > out.data
14 #end if 14 #else
15 -d out/ 15 "$input_file" -d out/
16 #end if
16 #end if 17 #end if
17 #if $input_file.is_of_type("tar"): 18 #if $input_file.is_of_type("tar"):
18 tar -xf "$input_file" 19 tar
19 #if $extract_options['extract_all'] == 'False' 20 #if $extract_options['extract_all'] == 'False'
20 "$extract_options['pathtofile']" 21 xfO "$input_file" "$extract_options['pathtofile']" > out.data
21 #end if 22 #else
22 -C ./out/ 23 -xf "$input_file" -C ./out/
24 #end if
23 #end if 25 #end if
24 ]]> 26 ]]>
25 </command> 27 </command>
26 <inputs> 28 <inputs>
27 <param label="input_file" name="input_file" type="data" format="zip,tar"/> 29 <param label="input_file" name="input_file" type="data" format="zip,tar"/>
28
29 <conditional name="extract_options"> 30 <conditional name="extract_options">
30 <param label="Extract single file" name="extract_all" type="select"> 31 <param label="Extract single file" name="extract_all" type="select">
31 <option selected="True" value="True">All files</option> 32 <option selected="True" value="True">All files</option>
32 <option value="False">Single file</option> 33 <option value="False">Single file</option>
33 </param> 34 </param>
34 <when value="True"></when> 35 <when value="True"></when>
35 <when value="False"> 36 <when value="False">
36 <param name="pathtofile" type="text" value="" label="Filepath"> 37 <param name="pathtofile" type="text" value="" label="Filepath">
37 <sanitizer invalid_char=""> 38 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
38 <valid initial="string.ascii_letters,string.digits"> 39 <validator type="expression" message="No comma (,) allowed">',' not in value</validator>
39 <add value="_" /> 40 <validator type="expression" message="No asterisk (*) allowed">'*' not in value</validator>
40 <add value="/" /> 41 <validator type="expression" message="No leading slash (/) allowed">str(value)[0] != '/'</validator>
41 <add value="." />
42 <add value="/../" />
43 </valid>
44 </sanitizer>
45 </param> 42 </param>
46 </when> 43 </when>
47 </conditional> 44 </conditional>
48 </inputs> 45 </inputs>
49 <outputs> 46 <outputs>
50 <data name="unzipped_single"> 47 <data auto_format="true" name="unzipped_single" from_work_dir="out.data">
51 <discover_datasets pattern="__name__" directory="out" visible="true" ext="data" assign_primary_output="true" />
52 <filter>extract_options['extract_all'] == 'False'</filter> 48 <filter>extract_options['extract_all'] == 'False'</filter>
53 </data> 49 </data>
54 <collection name="unzipped" type="list" label="${tool.name} on ${on_string}"> 50 <collection name="unzipped" type="list" label="${tool.name} on ${on_string}">
55 <discover_datasets pattern="__name__" ext="data" directory="out" visible="false"/> 51 <discover_datasets pattern="__designation_and_ext__" directory="out" visible="false" format="auto" />
56 <filter>extract_options['extract_all'] == 'True'</filter> 52 <filter>extract_options['extract_all'] == 'True'</filter>
57 </collection> 53 </collection>
58 </outputs> 54 </outputs>
59 <tests> 55 <tests>
60 <test> 56 <test>
61 <param name="input_file" value="input.zip" ftype="zip"/> 57 <param name="input_file" value="input.zip" ftype="zip"/>
62 <param name="extract_all" value="False"/> 58 <param name="extract_all" value="False"/>
63 <param name="pathtofile" value="input.png"/> 59 <param name="pathtofile" value="input.png"/>
64 <output name="unzipped_single" file="input.png" ftype="data" compare="sim_size" /> 60 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size" />
65 </test> 61 </test>
66 <test> 62 <test>
67 <param name="input_file" value="input.zip" ftype="zip"/> 63 <param name="input_file" value="input.zip" ftype="zip"/>
68 <param name="extract_all" value="True"/> 64 <param name="extract_all" value="True"/>
69 <output_collection name="unzipped" type="list"> 65 <output_collection name="unzipped" type="list">
70 <element name="input.png" file="input.png" ftype="data" compare="sim_size"/> 66 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
71 <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/> 67 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
72 </output_collection> 68 </output_collection>
73 </test> 69 </test>
74 <test> 70 <test>
75 <param name="input_file" value="input.tar" ftype="tar"/> 71 <param name="input_file" value="input.tar" ftype="tar"/>
76 <param name="extract_all" value="True"/> 72 <param name="extract_all" value="True"/>
77 <output_collection name="unzipped" type="list"> 73 <output_collection name="unzipped" type="list">
78 <element name="input.png" file="input.png" ftype="data" compare="sim_size"/> 74 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
79 <element name="res.tiff" file="res.tiff" ftype="data" compare="sim_size"/> 75 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
80 </output_collection> 76 </output_collection>
81 </test> 77 </test>
82 </tests> 78 </tests>
83 <help> 79 <help>
84 **What it does** 80 **What it does**