changeset 0:f71a1cb1a0d2 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/simple_tool.sh	Wed Jun 18 17:00:16 2014 -0400
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+INPUT="$1"
+OUTPUT="$2"
+
+echo $INPUT > $OUTPUT
+exit 0
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/simple_tool.xml	Wed Jun 18 17:00:16 2014 -0400
@@ -0,0 +1,43 @@
+<?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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jun 18 17:00:16 2014 -0400
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="simple_tool" version="1.0.0">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="SCRIPT_PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>whatever</readme>
+    </package>
+</tool_dependency>