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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:23:10 +0000
parents 5a8835c225a4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
imgteam
parents: 2
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1 <tool id="unzip" name="Unzip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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2 <description>Unzip a file</description>
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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3 <macros>
5
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4 <import>creators.xml</import>
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5 <token name="@TOOL_VERSION@">6.0</token>
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5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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6 <token name="@VERSION_SUFFIX@">2</token>
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7 <token name="@PROFILE@">22.01</token>
5
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8 <xml name="regex_sanitizer">
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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9 <sanitizer>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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10 <valid>
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11 <add preset="string.printable"/>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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12 <remove value="\"/>
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13 <remove value="'"/>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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14 </valid>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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15 <mapping initial="none">
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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16 <add source="\" target="__backslash__"/>
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17 <add source="'" target="__sq__"/>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
imgteam
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18 </mapping>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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19 </sanitizer>
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20 </xml>
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21 </macros>
5
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22 <creator>
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23 <expand macro="creators/bmcv"/>
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24 <expand macro="creators/tuncK"/>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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25 </creator>
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26 <requirements>
5
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27 <!--
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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28 BioContainer for: unzip=6.0,tar=1.34,findutils=4.10.0
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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29 Enforced containerization to minimize potential security issues due to regex hacking.
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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30 -->
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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31 <container type="docker">quay.io/biocontainers/mulled-v2-6a2891161dcf5f35b38c6a49fff923163de7a66d:159a5b483a078f27b97a401b0626abac09e5f2d1-0</container>
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d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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32 </requirements>
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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33 <command>
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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34 <![CDATA[
0
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35 mkdir ./out &&
11df4d6f9ab8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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36 #if $input_file.is_of_type("zip"):
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d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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37 unzip
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38 #if $extract_options['target'] == 'single'
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d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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39 -p '$input_file' '$extract_options["pathtofile"]' > out.data
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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40 #else
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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41 '$input_file' -d out/
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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42 #end if
0
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43 #end if
11df4d6f9ab8 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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44 #if $input_file.is_of_type("tar"):
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d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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45 tar
5
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46 #if $extract_options['target'] == 'single'
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47 xfO '$input_file' '$extract_options["pathtofile"]' > out.data
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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48 #else
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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49 -xf '$input_file' -C ./out/
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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50 #end if
0
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51 #end if
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52 &&
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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53
5
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54 ## Filter out files that do not match the regex
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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55 #if $extract_options['target'] != 'single'
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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56 pushd out &&
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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57 find . -regextype posix-extended -type f -not -regex '$extract_options["keep_regex"]' -delete &&
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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58 popd &&
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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59 #end if
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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60
3
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61 ## Flatten any potential directory structure, e.g.
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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62 ## out/sub1/subsub2/fileA.ext -> out/sub1_subsub2_fileA.ext
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63 find out -type f | cut -d '/' -f 2- | grep '/' | xargs -I % sh -c "mv out/% out/\\$(echo % | tr / _)"
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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64 ]]>
d3e92a93d671 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7
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65 </command>
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66 <inputs>
5
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67 <param label="Input file" name="input_file" type="data" format="zip,tar"/>
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68 <conditional name="extract_options">
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69 <param label="What to extract" name="target" type="select">
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e54b0e59b367 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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70 <option value="all" selected="True">All files</option>
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71 <option value="all_nondot">All files except dotfiles</option>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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72 <option value="all_regex">All files matching a regex</option>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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73 <option value="single">Single file</option>
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74 </param>
5
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75 <when value="all">
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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76 <param name="keep_regex" type="hidden" value=".*"/>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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77 </when>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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78 <when value="all_nondot">
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79 <param name="keep_regex" type="hidden" value=".*/[^.][^/]*">
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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80 <expand macro="regex_sanitizer"/>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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81 </param>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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82 </when>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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83 <when value="all_regex">
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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84 <param name="keep_regex" type="text" value=".*" optional="False" label="Regular expression" help="POSIX regular expression, that will be used for filtering the extracted files. Only files that match this expression will be retained. Example: To only retain files from a sub-directory &lt;tt&gt;subdir&lt;/tt&gt;, use &lt;tt&gt;./subdir/.*&lt;/tt&gt; as the regular expression.">
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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85 <expand macro="regex_sanitizer"/>
5a8835c225a4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
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86 </param>
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87 </when>
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88 <when value="single">
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89 <param name="pathtofile" type="text" value="" label="File path">
3
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90 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
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91 <validator type="expression" message="No comma (,) allowed">',' not in value</validator>
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92 <validator type="expression" message="No asterisk (*) allowed">'*' not in value</validator>
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93 <validator type="expression" message="No leading slash (/) allowed">str(value)[0] != '/'</validator>
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94 </param>
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95 </when>
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96 </conditional>
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97 </inputs>
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98 <outputs>
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99 <data auto_format="true" name="unzipped_single" from_work_dir="out.data" label="${tool.name} on ${on_string}">
5
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100 <filter>extract_options['target'] == 'single'</filter>
0
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101 </data>
3
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102 <collection name="unzipped" type="list" label="${tool.name} on ${on_string} all files as collection">
4
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103 <discover_datasets directory="out" pattern="(?P&lt;designation&gt;\.*[^\.]+)\.?(?P&lt;ext&gt;.*)" visible="false" format="auto"/>
5
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104 <filter>extract_options['target'] != 'single'</filter>
0
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105 </collection>
3
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106 </outputs>
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107 <tests>
4
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108 <test expect_num_outputs="1">
0
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109 <param name="input_file" value="input.zip" ftype="zip"/>
4
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110 <conditional name="extract_options">
5
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111 <param name="target" value="single"/>
4
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112 <param name="pathtofile" value="input.png"/>
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113 </conditional>
3
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114 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>
0
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115 </test>
3
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116 <test expect_num_outputs="1">
0
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117 <param name="input_file" value="input.zip" ftype="zip"/>
4
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118 <conditional name="extract_options">
5
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119 <param name="target" value="all"/>
4
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120 </conditional>
3
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121 <output_collection name="unzipped" type="list" count="2">
1
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122 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
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123 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
0
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124 </output_collection>
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125 </test>
3
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126 <!-- Binary files without file extension -->
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127 <test expect_num_outputs="1">
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128 <param name="input_file" value="input_binary.zip" ftype="zip"/>
4
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129 <conditional name="extract_options">
5
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130 <param name="target" value="all"/>
4
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131 </conditional>
3
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132 <output_collection name="unzipped" type="list" count="2">
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133 <element name="yelp" file="yelp" compare="sim_size"/>
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134 <element name="yes" file="yes" compare="sim_size"/>
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135 </output_collection>
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136 </test>
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137 <!-- Compressed object with subfolders, each containing files -->
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138 <test expect_num_outputs="1">
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139 <param name="input_file" value="subfolders.zip" ftype="zip"/>
4
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140 <conditional name="extract_options">
5
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141 <param name="target" value="all"/>
4
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142 </conditional>
3
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143 <output_collection name="unzipped" type="list" count="4">
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144 <element name="binaries_yelp" file="yelp" compare="sim_size"/>
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145 <element name="binaries_yes" file="yes" compare="sim_size"/>
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146 <element name="images_input" file="input.png" ftype="png" compare="sim_size"/>
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147 <element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/>
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148 </output_collection>
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149 </test>
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150 <test expect_num_outputs="1">
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151 <param name="input_file" value="input.tar" ftype="tar"/>
4
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152 <conditional name="extract_options">
5
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153 <param name="target" value="single"/>
4
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154 <param name="pathtofile" value="input.png"/>
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155 </conditional>
3
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156 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>
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157 </test>
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158 <test expect_num_outputs="1">
0
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159 <param name="input_file" value="input.tar" ftype="tar"/>
4
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160 <conditional name="extract_options">
5
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161 <param name="target" value="all"/>
4
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162 </conditional>
3
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163 <output_collection name="unzipped" type="list" count="2">
1
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164 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
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165 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
0
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166 </output_collection>
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167 </test>
5
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168 <!-- ZIP containing dotfiles and non-dotfiles -->
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169 <test expect_num_outputs="1">
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170 <param name="input_file" value="input_with_dotfiles.zip" ftype="zip"/>
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171 <conditional name="extract_options">
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172 <param name="target" value="all"/>
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173 </conditional>
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174 <output_collection name="unzipped" type="list" count="4">
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175 <element name=".dotfile">
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176 <assert_contents>
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177 <has_size value="0"/>
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178 </assert_contents>
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179 </element>
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180 <element name="nondotfile">
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181 <assert_contents>
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182 <has_size value="0"/>
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183 </assert_contents>
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184 </element>
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185 <element name="subdir_"><!-- The suffix `.dotfile` is recognized as the extension -->
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186 <assert_contents>
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187 <has_size value="0"/>
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188 </assert_contents>
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189 </element>
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190 <element name="subdir_nondotfile">
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191 <assert_contents>
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192 <has_size value="0"/>
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193 </assert_contents>
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194 </element>
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195 </output_collection>
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196 </test>
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197 <test expect_num_outputs="1">
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198 <param name="input_file" value="input_with_dotfiles.zip" ftype="zip"/>
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199 <conditional name="extract_options">
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200 <param name="target" value="all_nondot"/>
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201 </conditional>
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202 <output_collection name="unzipped" type="list" count="2">
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203 <element name="nondotfile">
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204 <assert_contents>
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205 <has_size value="0"/>
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206 </assert_contents>
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207 </element>
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208 <element name="subdir_nondotfile">
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209 <assert_contents>
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210 <has_size value="0"/>
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211 </assert_contents>
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212 </element>
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213 </output_collection>
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214 </test>
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215 <!-- Custom Regex -->
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216 <test expect_num_outputs="1">
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217 <param name="input_file" value="subfolders.zip" ftype="zip"/>
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218 <conditional name="extract_options">
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219 <param name="target" value="all_regex"/>
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220 <param name="keep_regex" value="./images/.*"/>
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221 </conditional>
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222 <output_collection name="unzipped" type="list" count="2">
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223 <element name="images_input" file="input.png" ftype="png" compare="sim_size"/>
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224 <element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/>
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225 </output_collection>
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226 </test>
4
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227 </tests>
3
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228 <help>
6
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229
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230 **Unzip an archive containing file(s) of various types.**
3
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231
6
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232 If multiple files are asked to be retained, the output will be a collection containing all files within the ZIP or TAR archive.
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233
3
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234 </help>
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235 <citations>
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236 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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237 </citations>
0
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238 </tool>