comparison export_local_file.xml @ 8:01687750c862 draft

Uploaded

7:e5a905df7e0b

<?xml version="1.0"?>
<tool id="export_local_file" name="Export dataset" version="1.1.0">
  <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" />
  </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.
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

-----

**Example**

8:01687750c862

<?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**