| Previous changeset 1:38eec75fbe9b (2019-08-02) |
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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit a8d89b9ebc13951944dcec84323464692837bba7 |
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modified:
unzip.xml |
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added:
test-data/input_binary.zip test-data/subfolders.zip test-data/yelp test-data/yes |
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| diff -r 38eec75fbe9b -r 57f0914ddb7b test-data/subfolders.zip |
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| Binary file test-data/subfolders.zip has changed |
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| diff -r 38eec75fbe9b -r 57f0914ddb7b test-data/yelp |
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| Binary file test-data/yelp has changed |
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| diff -r 38eec75fbe9b -r 57f0914ddb7b test-data/yes |
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| diff -r 38eec75fbe9b -r 57f0914ddb7b unzip.xml --- a/unzip.xml Fri Aug 02 07:21:01 2019 -0400 +++ b/unzip.xml Fri Apr 14 19:02:41 2023 +0000 |
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| b'@@ -1,88 +1,125 @@\n-<tool id="unzip" name="Unzip" version="0.2"> \n- <description>Unzip file</description>\n- <requirements>\n- <requirement type="package">unzip</requirement>\n- <requirement type="package">tar</requirement>\n- </requirements>\n- <command> \n- <![CDATA[ \n+<tool id="unzip" name="Unzip" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description>Unzip a file</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">6.0</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">22.01</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">unzip</requirement>\n+ <requirement type="package" version="1.34">tar</requirement>\n+ </requirements>\n+ <command> \n+ <![CDATA[\n mkdir ./out &&\n #if $input_file.is_of_type("zip"):\n- unzip\n- #if $extract_options[\'extract_all\'] == \'False\'\n- -p "$input_file" "$extract_options[\'pathtofile\']" > out.data\n- #else\n- "$input_file" -d out/\n- #end if\n+ unzip\n+ #if $extract_options[\'extract_all\'] == \'False\'\n+ -p \'$input_file\' \'$extract_options["pathtofile"]\' > out.data\n+ #else\n+ \'$input_file\' -d out/\n+ #end if\n #end if\n #if $input_file.is_of_type("tar"):\n- tar\n- #if $extract_options[\'extract_all\'] == \'False\'\n- xfO "$input_file" "$extract_options[\'pathtofile\']" > out.data\n- #else\n- -xf "$input_file" -C ./out/\n- #end if\n+ tar\n+ #if $extract_options[\'extract_all\'] == \'False\'\n+ xfO \'$input_file\' \'$extract_options["pathtofile"]\' > out.data\n+ #else\n+ -xf \'$input_file\' -C ./out/\n+ #end if\n #end if\n- ]]>\n- </command>\n- <inputs>\n- <param label="input_file" name="input_file" type="data" format="zip,tar"/>\n- <conditional name="extract_options">\n- <param label="Extract single file" name="extract_all" type="select">\n- <option selected="True" value="True">All files</option>\n- <option value="False">Single file</option>\n- </param>\n- <when value="True"></when>\n- <when value="False">\n- <param name="pathtofile" type="text" value="" label="Filepath">\n- <validator type="expression" message="No two dots (..) allowed">\'..\' not in value</validator>\n- <validator type="expression" message="No comma (,) allowed">\',\' not in value</validator>\n- <validator type="expression" message="No asterisk (*) allowed">\'*\' not in value</validator>\n- <validator type="expression" message="No leading slash (/) allowed">str(value)[0] != \'/\'</validator>\n- </param>\n- </when>\n- </conditional>\n- </inputs>\n- <outputs>\n- <data auto_format="true" name="unzipped_single" from_work_dir="out.data">\n- <filter>extract_options[\'extract_all\'] == \'False\'</filter>\n+ &&\n+\n+ ## Flatten any potential directory structure, e.g.\n+ ## out/sub1/subsub2/fileA.ext -> out/sub1_subsub2_fileA.ext\n+ find out -type f | cut -d \'/\' -f 2- | grep \'/\' | xargs -I % sh -c "mv out/% out/\\\\$(echo % | tr / _)"\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param label="input_file" name="input_file" type="data" format="zip,tar"/>\n+ <conditional name="extract_options">\n+ <param label="Extract single file" name="extract_all" type="select">\n+ <option selected="True" value="True">All files</option>\n+ <option value="False">Single file</option>\n+ </param>\n+ <when value="True"></when>\n+ <when value="False">\n+ <param name="pathtofile" type="text" value="" label="Filepath">\n+ <validator type="expression" message="No two dots (..) allowed">\'..\' not in value</validator>\n+ '..b'tion>.+?)(\\.(?P<ext>[^\\._]+))?$" visible="false" format="auto"/>\n+ <!-- pattern=__designation_and_ext__ = (?P<designation>.*)\\.(?P<ext>[^\\._]+)? would discard files without extensions -->\n+ <filter>extract_options[\'extract_all\'] == \'True\'</filter>\n </collection>\n- </outputs>\n- <tests>\n- <test>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n <param name="input_file" value="input.zip" ftype="zip"/>\n <param name="extract_all" value="False"/>\n <param name="pathtofile" value="input.png"/>\n- <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size" />\n+ <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <param name="input_file" value="input.zip" ftype="zip"/>\n <param name="extract_all" value="True"/>\n- <output_collection name="unzipped" type="list">\n+ <output_collection name="unzipped" type="list" count="2">\n <element name="input" file="input.png" ftype="png" compare="sim_size"/>\n <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>\n </output_collection>\n </test>\n- <test>\n+ <!-- Binary files without file extension -->\n+ <test expect_num_outputs="1">\n+ <param name="input_file" value="input_binary.zip" ftype="zip"/>\n+ <param name="extract_all" value="True"/>\n+ <output_collection name="unzipped" type="list" count="2">\n+ <element name="yelp" file="yelp" compare="sim_size"/>\n+ <element name="yes" file="yes" compare="sim_size"/>\n+ </output_collection>\n+ </test>\n+ <!-- Compressed object with subfolders, each containing files -->\n+ <test expect_num_outputs="1">\n+ <param name="input_file" value="subfolders.zip" ftype="zip"/>\n+ <param name="extract_all" value="True"/>\n+ <output_collection name="unzipped" type="list" count="4">\n+ <element name="binaries_yelp" file="yelp" compare="sim_size"/>\n+ <element name="binaries_yes" file="yes" compare="sim_size"/>\n+ <element name="images_input" file="input.png" ftype="png" compare="sim_size"/>\n+ <element name="images_res" file="res.tiff" ftype="tiff" compare="sim_size"/>\n+ </output_collection>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="input_file" value="input.tar" ftype="tar"/>\n+ <param name="extract_all" value="False"/>\n+ <param name="pathtofile" value="input.png"/>\n+ <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size"/>\n+ </test>\n+ <test expect_num_outputs="1">\n <param name="input_file" value="input.tar" ftype="tar"/>\n <param name="extract_all" value="True"/>\n- <output_collection name="unzipped" type="list">\n+ <output_collection name="unzipped" type="list" count="2">\n <element name="input" file="input.png" ftype="png" compare="sim_size"/>\n <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>\n </output_collection>\n </test>\n- </tests> \n- <help>\n- **What it does**\n-\n- Unzip folder to collection.\n- </help>\n- <citations>\n- <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>\n- </citations>\n+ </tests> \n+ <help>\n+ **What it does**\n+ \n+ 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.\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>\n+ </citations>\n </tool>\n \n' |