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1 <?xml version="1.0"?>
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2 <tool id="simple_tool" name="Simple Tool" version="1.0.0">
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3 <description>Simple Tool</description>
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4 <requirements>
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5 <requirement type="set_environment">SCRIPT_PATH</requirement>
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6 </requirements>
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7 <command interpreter="sh">simple_tool.sh '$filepath' $output</command>
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8 <inputs>
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9 <param name="filepath" type="text" size="100" label="anything" value="/home/foo/blah">
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10 </param>
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11
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="output" label="whatever" />
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15 </outputs>
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16 <help>
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17
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18 .. class:: infomark
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19
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20 **Copying files**
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21
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22 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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23 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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24
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25 .. class:: warningmark
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26
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27 **Important Notes**
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28
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29 - The file path must be a file, not a directory
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30 - You must give the fullpath to the file (/home/user/myfile.txt, not ./myfile.txt)
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31 - You must have permission to read the file
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32 - Only /home or /data directories are allowed
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33 - The files must be on Helix or Biowulf! Use 'Upload File' for all other files!
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34
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35 -----
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36
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37 **Example**
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38
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39 - /home/user/bamfiles/abc123.bam
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40 - /data/anotheruser/data/good_data/very_good_data.txt
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41
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42 </help>
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43 </tool>
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