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annotate unzip.xml @ 1:38eec75fbe9b draft

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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
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1
38eec75fbe9b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit ab38debe1175446664e9bede9be8c667894bf9f1
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1 <tool id="unzip" name="Unzip" version="0.2">
0
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2 <description>Unzip file</description>
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3 <requirements>
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4 <requirement type="package">unzip</requirement>
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5 <requirement type="package">tar</requirement>
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6 </requirements>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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7 <command>
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8 <![CDATA[
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9 mkdir ./out &&
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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10 #if $input_file.is_of_type("zip"):
1
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11 unzip
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12 #if $extract_options['extract_all'] == 'False'
38eec75fbe9b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit ab38debe1175446664e9bede9be8c667894bf9f1
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13 -p "$input_file" "$extract_options['pathtofile']" > out.data
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14 #else
38eec75fbe9b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit ab38debe1175446664e9bede9be8c667894bf9f1
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15 "$input_file" -d out/
38eec75fbe9b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit ab38debe1175446664e9bede9be8c667894bf9f1
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16 #end if
0
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17 #end if
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18 #if $input_file.is_of_type("tar"):
1
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19 tar
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20 #if $extract_options['extract_all'] == 'False'
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21 xfO "$input_file" "$extract_options['pathtofile']" > out.data
38eec75fbe9b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit ab38debe1175446664e9bede9be8c667894bf9f1
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22 #else
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23 -xf "$input_file" -C ./out/
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24 #end if
0
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25 #end if
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26 ]]>
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27 </command>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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28 <inputs>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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29 <param label="input_file" name="input_file" type="data" format="zip,tar"/>
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30 <conditional name="extract_options">
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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31 <param label="Extract single file" name="extract_all" type="select">
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32 <option selected="True" value="True">All files</option>
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33 <option value="False">Single file</option>
ec30427e0d42 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit 2183b20497f6ed7962ae764c7a93d0adcfffe254
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34 </param>
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35 <when value="True"></when>
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36 <when value="False">
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37 <param name="pathtofile" type="text" value="" label="Filepath">
1
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38 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
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39 <validator type="expression" message="No comma (,) allowed">',' not in value</validator>
38eec75fbe9b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit ab38debe1175446664e9bede9be8c667894bf9f1
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40 <validator type="expression" message="No asterisk (*) allowed">'*' not in value</validator>
38eec75fbe9b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/unzip/ commit ab38debe1175446664e9bede9be8c667894bf9f1
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41 <validator type="expression" message="No leading slash (/) allowed">str(value)[0] != '/'</validator>
0
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42 </param>
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43 </when>
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44 </conditional>
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45 </inputs>
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46 <outputs>
1
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47 <data auto_format="true" name="unzipped_single" from_work_dir="out.data">
0
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48 <filter>extract_options['extract_all'] == 'False'</filter>
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49 </data>
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50 <collection name="unzipped" type="list" label="${tool.name} on ${on_string}">
1
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51 <discover_datasets pattern="__designation_and_ext__" directory="out" visible="false" format="auto" />
0
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52 <filter>extract_options['extract_all'] == 'True'</filter>
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53 </collection>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input_file" value="input.zip" ftype="zip"/>
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58 <param name="extract_all" value="False"/>
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59 <param name="pathtofile" value="input.png"/>
1
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60 <output name="unzipped_single" file="input.png" ftype="png" compare="sim_size" />
0
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61 </test>
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62 <test>
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63 <param name="input_file" value="input.zip" ftype="zip"/>
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64 <param name="extract_all" value="True"/>
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65 <output_collection name="unzipped" type="list">
1
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66 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
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67 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
0
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68 </output_collection>
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69 </test>
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70 <test>
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71 <param name="input_file" value="input.tar" ftype="tar"/>
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72 <param name="extract_all" value="True"/>
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73 <output_collection name="unzipped" type="list">
1
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74 <element name="input" file="input.png" ftype="png" compare="sim_size"/>
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75 <element name="res" file="res.tiff" ftype="tiff" compare="sim_size"/>
0
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76 </output_collection>
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77 </test>
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78 </tests>
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79 <help>
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80 **What it does**
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81
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82 Unzip folder to collection.
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83 </help>
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84 <citations>
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85 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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86 </citations>
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87 </tool>
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88