Mercurial > repos > imgteam > unzip
changeset 4:28d6129b2901 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/ commit 76ea79c003386720807ac7a4f01da9248856cc5c
| author | imgteam |
|---|---|
| date | Mon, 06 Oct 2025 10:17:01 +0000 |
| parents | 4634764e6e2b |
| children | |
| files | creators.xml test-data/input_with_dotfiles.zip unzip.xml |
| diffstat | 3 files changed, 159 insertions(+), 20 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Mon Oct 06 10:17:01 2025 +0000 @@ -0,0 +1,38 @@ +<macros> + + <xml name="creators/bmcv"> + <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" /> + <yield /> + </xml> + + <xml name="creators/rmassei"> + <person givenName="Riccardo" familyName="Massei"/> + <yield/> + </xml> + + <xml name="creators/alliecreason"> + <person givenName="Allison" familyName="Creason"/> + <yield/> + </xml> + + <xml name="creators/bugraoezdemir"> + <person givenName="Bugra" familyName="Oezdemir"/> + <yield/> + </xml> + + <xml name="creators/thawn"> + <person givenName="Till" familyName="Korten"/> + <yield/> + </xml> + + <xml name="creators/pavanvidem"> + <person givenName="Pavan" familyName="Videm"/> + <yield/> + </xml> + + <xml name="creators/tuncK"> + <person givenName="Tunc" familyName="Kayikcioglu"/> + <yield/> + </xml> + +</macros>
--- a/unzip.xml Fri Sep 26 09:16:40 2025 +0000 +++ b/unzip.xml Mon Oct 06 10:17:01 2025 +0000 @@ -1,20 +1,41 @@ <tool id="unzip" name="Unzip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Unzip a file</description> <macros> + <import>creators.xml</import> <token name="@TOOL_VERSION@">6.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.01</token> + <xml name="regex_sanitizer"> + <sanitizer> + <valid> + <add preset="string.printable"/> + <remove value="\"/> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="\" target="__backslash__"/> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </xml> </macros> + <creator> + <expand macro="creators/bmcv"/> + <expand macro="creators/tuncK"/> + </creator> <requirements> - <requirement type="package" version="@TOOL_VERSION@">unzip</requirement> - <requirement type="package" version="1.34">tar</requirement> + <!-- + BioContainer for: unzip=6.0,tar=1.34,findutils=4.10.0 + Enforced containerization to minimize potential security issues due to regex hacking. + --> + <container type="docker">quay.io/biocontainers/mulled-v2-6a2891161dcf5f35b38c6a49fff923163de7a66d:159a5b483a078f27b97a401b0626abac09e5f2d1-0</container> </requirements> <command> <![CDATA[ mkdir ./out && #if $input_file.is_of_type("zip"): unzip - #if $extract_options['extract_all'] == 'False' + #if $extract_options['target'] == 'single' -p '$input_file' '$extract_options["pathtofile"]' > out.data #else '$input_file' -d out/ @@ -22,7 +43,7 @@ #end if #if $input_file.is_of_type("tar"): tar - #if $extract_options['extract_all'] == 'False' + #if $extract_options['target'] == 'single' xfO '$input_file' '$extract_options["pathtofile"]' > out.data #else -xf '$input_file' -C ./out/ @@ -30,21 +51,42 @@ #end if && + ## Filter out files that do not match the regex + #if $extract_options['target'] != 'single' + pushd out && + find . -regextype posix-extended -type f -not -regex '$extract_options["keep_regex"]' -delete && + popd && + #end if + ## Flatten any potential directory structure, e.g. ## out/sub1/subsub2/fileA.ext -> out/sub1_subsub2_fileA.ext find out -type f | cut -d '/' -f 2- | grep '/' | xargs -I % sh -c "mv out/% out/\\$(echo % | tr / _)" ]]> </command> <inputs> - <param label="input_file" name="input_file" type="data" format="zip,tar"/> + <param label="Input file" name="input_file" type="data" format="zip,tar"/> <conditional name="extract_options"> - <param label="Extract single file" name="extract_all" type="select"> - <option selected="True" value="True">All files</option> - <option value="False">Single file</option> + <param label="What to extract" name="target" type="select"> + <option selected="True" value="all">All files</option> + <option value="all_nondot">All files except dotfiles</option> + <option value="all_regex">All files matching a regex</option> + <option value="single">Single file</option> </param> - <when value="True"/> - <when value="False"> - <param name="pathtofile" type="text" value="" label="Filepath"> + <when value="all"> + <param name="keep_regex" type="hidden" value=".*"/> + </when> + <when value="all_nondot"> + <param name="keep_regex" type="hidden" value=".*/[^.][^/]*"> + <expand macro="regex_sanitizer"/> + </param> + </when> + <when value="all_regex"> + <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 <tt>subdir</tt>, use <tt>./subdir/.*</tt> as the regular expression."> + <expand macro="regex_sanitizer"/> + </param> + </when> + <when value="single"> + <param name="pathtofile" type="text" value="" label="File path"> <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> <validator type="expression" message="No comma (,) allowed">',' not in value</validator> <validator type="expression" message="No asterisk (*) allowed">'*' not in value</validator> @@ -55,18 +97,18 @@ </inputs> <outputs> <data auto_format="true" name="unzipped_single" from_work_dir="out.data" label="${tool.name} on ${on_string}"> - <filter>extract_options['extract_all'] == 'False'</filter> + <filter>extract_options['target'] == 'single'</filter> </data> <collection name="unzipped" type="list" label="${tool.name} on ${on_string} all files as collection"> <discover_datasets directory="out" pattern="(?P<designation>\.*[^\.]+)\.?(?P<ext>.*)" visible="false" format="auto"/> - <filter>extract_options['extract_all'] == 'True'</filter> + <filter>extract_options['target'] != 'single'</filter> </collection> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_file" value="input.zip" ftype="zip"/> <conditional name="extract_options"> - <param name="extract_all" value="False"/> + <param name="target" value="single"/> <param name="pathtofile" value="input.png"/> </conditional> <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/> @@ -74,7 +116,7 @@ <test expect_num_outputs="1"> <param name="input_file" value="input.zip" ftype="zip"/> <conditional name="extract_options"> - <param name="extract_all" value="True"/> + <param name="target" value="all"/> </conditional> <output_collection name="unzipped" type="list" count="2"> <element name="input" file="input.png" ftype="png" compare="sim_size"/> @@ -85,7 +127,7 @@ <test expect_num_outputs="1"> <param name="input_file" value="input_binary.zip" ftype="zip"/> <conditional name="extract_options"> - <param name="extract_all" value="True"/> + <param name="target" value="all"/> </conditional> <output_collection name="unzipped" type="list" count="2"> <element name="yelp" file="yelp" compare="sim_size"/> @@ -96,7 +138,7 @@ <test expect_num_outputs="1"> <param name="input_file" value="subfolders.zip" ftype="zip"/> <conditional name="extract_options"> - <param name="extract_all" value="True"/> + <param name="target" value="all"/> </conditional> <output_collection name="unzipped" type="list" count="4"> <element name="binaries_yelp" file="yelp" compare="sim_size"/> @@ -108,7 +150,7 @@ <test expect_num_outputs="1"> <param name="input_file" value="input.tar" ftype="tar"/> <conditional name="extract_options"> - <param name="extract_all" value="False"/> + <param name="target" value="single"/> <param name="pathtofile" value="input.png"/> </conditional> <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/> @@ -116,13 +158,72 @@ <test expect_num_outputs="1"> <param name="input_file" value="input.tar" ftype="tar"/> <conditional name="extract_options"> - <param name="extract_all" value="True"/> + <param name="target" value="all"/> </conditional> <output_collection name="unzipped" type="list" count="2"> <element name="input" file="input.png" ftype="png" compare="sim_size"/> <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/> </output_collection> </test> + <!-- ZIP containing dotfiles and non-dotfiles --> + <test expect_num_outputs="1"> + <param name="input_file" value="input_with_dotfiles.zip" ftype="zip"/> + <conditional name="extract_options"> + <param name="target" value="all"/> + </conditional> + <output_collection name="unzipped" type="list" count="4"> + <element name=".dotfile"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </element> + <element name="nondotfile"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </element> + <element name="subdir_"><!-- The suffix `.dotfile` is recognized as the extension --> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </element> + <element name="subdir_nondotfile"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="1"> + <param name="input_file" value="input_with_dotfiles.zip" ftype="zip"/> + <conditional name="extract_options"> + <param name="target" value="all_nondot"/> + </conditional> + <output_collection name="unzipped" type="list" count="2"> + <element name="nondotfile"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </element> + <element name="subdir_nondotfile"> + <assert_contents> + <has_size value="0"/> + </assert_contents> + </element> + </output_collection> + </test> + <!-- Custom Regex --> + <test expect_num_outputs="1"> + <param name="input_file" value="subfolders.zip" ftype="zip"/> + <conditional name="extract_options"> + <param name="target" value="all_regex"/> + <param name="keep_regex" value="./images/.*"/> + </conditional> + <output_collection name="unzipped" type="list" count="2"> + <element name="images_input" file="input.png" ftype="png" compare="sim_size"/> + <element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/> + </output_collection> + </test> </tests> <help> **What it does**