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1 <?xml version="1.0"?>
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2 <tool id="export_local_file" name="Export dataset" version="1.2.0">
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3 <description>to a local filesytem</description>
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4 <command interpreter="sh">export_local_file.sh $input '$filepath' $userEmail $output</command>
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5 <inputs>
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6 <param name="input" type="data" label="Dataset"/>
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7 <param name="filepath" type="text" size="100" label="Absolute file path" value="/home/foo/blah">
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8 <validator type="expression" message="The path must begin with either /home or /data">value.lower()[0:5] == '/home' or value.lower()[0:5] == '/data'</validator>
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9 </param>
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10 </inputs>
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11 <outputs>
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12 <data format="txt" name="output" label="local export: $filepath" />
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13 </outputs>
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14 <help>
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15
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16 .. class:: infomark
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17
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18 **Copying files**
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19
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20 This tool will allow you to export a single file from Galaxy to a local filesystem on Helix or Biowulf.
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21 You must have permission to write the file to the given directory, and the file must not yet exist. This tool will
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22 not overwrite a pre-existing file.
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23
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24 .. class:: warningmark
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25
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26 **Important Notes**
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27
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28 - The file path must be a file, not a directory
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29 - You must give the fullpath to the file (/home/user/myfile.txt, not ./myfile.txt)
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30 - You must have permission to write the file in the given directory
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31 - Only /home or /data directories are allowed.
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32 - The directories must exist on Helix or Biowulf!
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33
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34 -----
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35
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36 **Example**
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37
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38 - /home/user/bamfiles/abc123.bam
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39 - /data/anotheruser/data/good_data/very_good_data.txt
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40
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41 </help>
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42 </tool>
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