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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
author imgteam
date Fri, 14 Apr 2023 19:02:41 +0000
parents 38eec75fbe9b
children
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1:38eec75fbe9b 2:57f0914ddb7b
1 <tool id="unzip" name="Unzip" version="0.2"> 1 <tool id="unzip" name="Unzip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Unzip file</description> 2 <description>Unzip a file</description>
3 <requirements> 3 <macros>
4 <requirement type="package">unzip</requirement> 4 <token name="@TOOL_VERSION@">6.0</token>
5 <requirement type="package">tar</requirement> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </requirements> 6 <token name="@PROFILE@">22.01</token>
7 <command> 7 </macros>
8 <![CDATA[ 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">unzip</requirement>
10 <requirement type="package" version="1.34">tar</requirement>
11 </requirements>
12 <command>
13 <![CDATA[
9 mkdir ./out && 14 mkdir ./out &&
10 #if $input_file.is_of_type("zip"): 15 #if $input_file.is_of_type("zip"):
11 unzip 16 unzip
12 #if $extract_options['extract_all'] == 'False' 17 #if $extract_options['extract_all'] == 'False'
13 -p "$input_file" "$extract_options['pathtofile']" > out.data 18 -p '$input_file' '$extract_options["pathtofile"]' > out.data
14 #else 19 #else
15 "$input_file" -d out/ 20 '$input_file' -d out/
16 #end if 21 #end if
17 #end if 22 #end if
18 #if $input_file.is_of_type("tar"): 23 #if $input_file.is_of_type("tar"):
19 tar 24 tar
20 #if $extract_options['extract_all'] == 'False' 25 #if $extract_options['extract_all'] == 'False'
21 xfO "$input_file" "$extract_options['pathtofile']" > out.data 26 xfO '$input_file' '$extract_options["pathtofile"]' > out.data
22 #else 27 #else
23 -xf "$input_file" -C ./out/ 28 -xf '$input_file' -C ./out/
24 #end if 29 #end if
25 #end if 30 #end if
26 ]]> 31 &&
27 </command> 32
28 <inputs> 33 ## Flatten any potential directory structure, e.g.
29 <param label="input_file" name="input_file" type="data" format="zip,tar"/> 34 ## out/sub1/subsub2/fileA.ext -> out/sub1_subsub2_fileA.ext
30 <conditional name="extract_options"> 35 find out -type f | cut -d '/' -f 2- | grep '/' | xargs -I % sh -c "mv out/% out/\\$(echo % | tr / _)"
31 <param label="Extract single file" name="extract_all" type="select"> 36 ]]>
32 <option selected="True" value="True">All files</option> 37 </command>
33 <option value="False">Single file</option> 38 <inputs>
34 </param> 39 <param label="input_file" name="input_file" type="data" format="zip,tar"/>
35 <when value="True"></when> 40 <conditional name="extract_options">
36 <when value="False"> 41 <param label="Extract single file" name="extract_all" type="select">
37 <param name="pathtofile" type="text" value="" label="Filepath"> 42 <option selected="True" value="True">All files</option>
38 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> 43 <option value="False">Single file</option>
39 <validator type="expression" message="No comma (,) allowed">',' not in value</validator> 44 </param>
40 <validator type="expression" message="No asterisk (*) allowed">'*' not in value</validator> 45 <when value="True"></when>
41 <validator type="expression" message="No leading slash (/) allowed">str(value)[0] != '/'</validator> 46 <when value="False">
42 </param> 47 <param name="pathtofile" type="text" value="" label="Filepath">
43 </when> 48 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
44 </conditional> 49 <validator type="expression" message="No comma (,) allowed">',' not in value</validator>
45 </inputs> 50 <validator type="expression" message="No asterisk (*) allowed">'*' not in value</validator>
46 <outputs> 51 <validator type="expression" message="No leading slash (/) allowed">str(value)[0] != '/'</validator>
47 <data auto_format="true" name="unzipped_single" from_work_dir="out.data"> 52 </param>
48 <filter>extract_options['extract_all'] == 'False'</filter> 53 </when>
54 </conditional>
55 </inputs>
56 <outputs>
57 <data auto_format="true" name="unzipped_single" from_work_dir="out.data" label="${tool.name} on ${on_string}">
58 <filter>extract_options['extract_all'] == 'False'</filter>
49 </data> 59 </data>
50 <collection name="unzipped" type="list" label="${tool.name} on ${on_string}"> 60 <collection name="unzipped" type="list" label="${tool.name} on ${on_string} all files as collection">
51 <discover_datasets pattern="__designation_and_ext__" directory="out" visible="false" format="auto" /> 61 <discover_datasets directory="out" pattern="(?P&lt;designation&gt;.+?)(\.(?P&lt;ext&gt;[^\._]+))?$" visible="false" format="auto"/>
52 <filter>extract_options['extract_all'] == 'True'</filter> 62 <!-- pattern=__designation_and_ext__ = (?P&lt;designation&gt;.*)\.(?P&lt;ext&gt;[^\._]+)? would discard files without extensions -->
63 <filter>extract_options['extract_all'] == 'True'</filter>
53 </collection> 64 </collection>
54 </outputs> 65 </outputs>
55 <tests> 66 <tests>
56 <test> 67 <test expect_num_outputs="1">
57 <param name="input_file" value="input.zip" ftype="zip"/> 68 <param name="input_file" value="input.zip" ftype="zip"/>
58 <param name="extract_all" value="False"/> 69 <param name="extract_all" value="False"/>
59 <param name="pathtofile" value="input.png"/> 70 <param name="pathtofile" value="input.png"/>
60 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size" /> 71 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>
61 </test> 72 </test>
62 <test> 73 <test expect_num_outputs="1">
63 <param name="input_file" value="input.zip" ftype="zip"/> 74 <param name="input_file" value="input.zip" ftype="zip"/>
64 <param name="extract_all" value="True"/> 75 <param name="extract_all" value="True"/>
65 <output_collection name="unzipped" type="list"> 76 <output_collection name="unzipped" type="list" count="2">
66 <element name="input" file="input.png" ftype="png" compare="sim_size"/> 77 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
67 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/> 78 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
68 </output_collection> 79 </output_collection>
69 </test> 80 </test>
70 <test> 81 <!-- Binary files without file extension -->
82 <test expect_num_outputs="1">
83 <param name="input_file" value="input_binary.zip" ftype="zip"/>
84 <param name="extract_all" value="True"/>
85 <output_collection name="unzipped" type="list" count="2">
86 <element name="yelp" file="yelp" compare="sim_size"/>
87 <element name="yes" file="yes" compare="sim_size"/>
88 </output_collection>
89 </test>
90 <!-- Compressed object with subfolders, each containing files -->
91 <test expect_num_outputs="1">
92 <param name="input_file" value="subfolders.zip" ftype="zip"/>
93 <param name="extract_all" value="True"/>
94 <output_collection name="unzipped" type="list" count="4">
95 <element name="binaries_yelp" file="yelp" compare="sim_size"/>
96 <element name="binaries_yes" file="yes" compare="sim_size"/>
97 <element name="images_input" file="input.png" ftype="png" compare="sim_size"/>
98 <element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/>
99 </output_collection>
100 </test>
101 <test expect_num_outputs="1">
102 <param name="input_file" value="input.tar" ftype="tar"/>
103 <param name="extract_all" value="False"/>
104 <param name="pathtofile" value="input.png"/>
105 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>
106 </test>
107 <test expect_num_outputs="1">
71 <param name="input_file" value="input.tar" ftype="tar"/> 108 <param name="input_file" value="input.tar" ftype="tar"/>
72 <param name="extract_all" value="True"/> 109 <param name="extract_all" value="True"/>
73 <output_collection name="unzipped" type="list"> 110 <output_collection name="unzipped" type="list" count="2">
74 <element name="input" file="input.png" ftype="png" compare="sim_size"/> 111 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
75 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/> 112 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
76 </output_collection> 113 </output_collection>
77 </test> 114 </test>
78 </tests> 115 </tests>
79 <help> 116 <help>
80 **What it does** 117 **What it does**
81 118
82 Unzip folder to collection. 119 Unzip a folder containing file(s) of various types. If multiple files are asked to be retained, the output will be a collection containing all files within the zip or tar archive.
83 </help> 120 </help>
84 <citations> 121 <citations>
85 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 122 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
86 </citations> 123 </citations>
87 </tool> 124 </tool>
88 125