Mercurial > repos > david-hoover > local_file_tools
view export_local_file.xml @ 9:8d6bf2bd8932 draft default tip
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| author | david-hoover |
|---|---|
| date | Tue, 13 May 2014 15:25:51 -0400 |
| parents | 01687750c862 |
| children |
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<?xml version="1.0"?> <tool id="export_local_file" name="Export dataset" version="1.2.0"> <description>to a local filesytem</description> <command interpreter="sh">export_local_file.sh $input '$filepath' $userEmail $output</command> <inputs> <param name="input" type="data" label="Dataset"/> <param name="filepath" type="text" size="100" label="Absolute file path" value="/home/foo/blah"> <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> </param> </inputs> <outputs> <data format="txt" name="output" label="local export: $filepath" /> </outputs> <help> .. class:: infomark **Copying files** This tool will allow you to export a single file from Galaxy to a local filesystem on Helix or Biowulf. You must have permission to write the file to the given directory, and the file must not yet exist. This tool will not overwrite a pre-existing file. .. class:: warningmark **Important Notes** - The file path must be a file, not a directory - You must give the fullpath to the file (/home/user/myfile.txt, not ./myfile.txt) - You must have permission to write the file in the given directory - Only /home or /data directories are allowed. - The directories must exist on Helix or Biowulf! ----- **Example** - /home/user/bamfiles/abc123.bam - /data/anotheruser/data/good_data/very_good_data.txt </help> </tool>
