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1 <?xml version="1.0"?>
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2 <tool id="import_local_file" name="Import local file" version="1.2.0">
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3 <description>from a local filesystem</description>
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4 <command interpreter="sh">import_local_file.sh '$filepath' $output $userEmail</command>
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5 <inputs>
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6 <param name="filepath" type="text" size="100" label="Absolute file path" value="/home/foo/blah">
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7 <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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8 </param>
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9
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10 </inputs>
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11 <outputs>
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12 <data format="txt" name="output" label="local import: $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 upload a single file that is locally available on Helix or Biowulf. There is no browse function,
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21 however, so you will need to give the full path name. If you have permission to read the file, Galaxy can import the file.
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22
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23 .. class:: warningmark
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24
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25 **Important Notes**
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26
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27 - The file path must be a file, not a directory
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28 - You must give the fullpath to the file (/home/user/myfile.txt, not ./myfile.txt)
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29 - You must have permission to read the file
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30 - Only /home or /data directories are allowed
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31 - The files must be on Helix or Biowulf! Use 'Upload File' for all other files!
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32
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33 -----
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34
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35 **Example**
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36
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37 - /home/user/bamfiles/abc123.bam
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38 - /data/anotheruser/data/good_data/very_good_data.txt
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39
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40 </help>
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41 </tool>
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