view simple_tool.xml @ 0:f71a1cb1a0d2 draft

Uploaded

<?xml version="1.0"?>
<tool id="simple_tool" name="Simple Tool" version="1.0.0">
  <description>Simple Tool</description>
  <requirements>
     <requirement type="set_environment">SCRIPT_PATH</requirement>
  </requirements>
  <command interpreter="sh">simple_tool.sh '$filepath' $output</command>
  <inputs>   
    <param name="filepath" type="text" size="100" label="anything" value="/home/foo/blah">
    </param>
      
  </inputs>
  <outputs> 
    <data format="txt" name="output" label="whatever" />
  </outputs>
  <help>

.. class:: infomark

**Copying files**

This tool will allow you to upload a single file that is locally available on Helix or Biowulf.  There is no browse function,
however, so you will need to give the full path name.  If you have permission to read the file, Galaxy can import the 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 read the file
- Only /home or /data directories are allowed
- The files must be on Helix or Biowulf!  Use 'Upload File' for all other files!

-----

**Example**

- /home/user/bamfiles/abc123.bam
- /data/anotheruser/data/good_data/very_good_data.txt

  </help>
</tool>