--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scriptrunner.xml	Sat Jul 09 16:57:13 2016 -0400
@@ -0,0 +1,127 @@
+<tool id="docker_scriptrunner" name="docker scriptrunner" version="0.1.6">
+  <description>Runs scripts using docker</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+   <requirements>
+      <requirement type="package" version="0.4.0">docker-py</requirement>
+  </requirements>
+  <command>
+    python "$__tool_directory__/scriptrunner.py"
+    --script_path "$runme"
+    --interpreter "$interpreter"
+    --user_email "$__user_email__"
+    #if $generate_simple_output.make_TAB=="yes":
+       --output_tab "$tab_file"
+    #end if
+    #if $make_HTML.value=="yes":
+      --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
+    #else:
+       --output_dir "."
+    #end if
+    #if $additional_parameters != 'None':
+      #for i in $additional_parameters:
+	--additional_parameters
+        "$i.param_name, $i.param_value"
+      #end for
+    #end if
+    #if $input_files != 'None':
+       --input_tab 
+	#for i in $input_files:
+	  $i.input
+	#end for
+        #for i in $input_files:
+          --input_format "Any"
+        #end for
+    #end if
+    --docker_image "$docker_image" 
+  </command>
+<configfiles>
+  <configfile name="runme">$dynScript</configfile>
+</configfiles>
+  <inputs>
+    <repeat name="input_files" title="Select input files">
+      <param name="input" format="data" type="data"  label="Select an input file from your history" optional="true" size="120"
+         help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
+    </repeat>
+    <repeat name="additional_parameters" title="Set additional parameters">
+      <param name="param_name" type="text" value="parameter_name" label="Choose a parameter name" size="20">
+        <sanitizer invalid_char="">
+          <valid initial="string.letters,string.digits"><add value="@_."/></valid>>
+        </sanitizer>
+      </param>
+     <param name="param_value" type="text" value="parameter_value" label="Enter a parameter value" size="50">
+       <sanitizer>
+         <valid initial="string.printable">
+         </valid>
+         <mapping initial="none"/>
+       </sanitizer>
+     </param>
+    </repeat> 
+    <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
+         help="Recommended for presenting complex outputs in an accessible manner. Turn off for simple tools so they just create one output">
+        <option value="yes">Yes, arrange all outputs produced by my script as an HTML output</option>
+        <option value="" selected="true">No, no HTML output file thanks</option>
+    </param>
+    <conditional name="generate_simple_output">
+      <param name="make_TAB" type="select" label="Create a new history output alongside the HTML file specified above" 
+           help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes">
+          <option value="yes" selected="true">My script writes to a new history output</option>
+          <option value="">I do not want a new history output file</option>
+      </param>
+      <when value="yes">
+        <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
+          <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+            <column name="value" index="0"/>
+          </options>
+        </param>
+      </when>
+      <when value="">
+      </when>
+    </conditional>
+    <param name="interpreter" type="select" label="Select the interpreter for your code">
+        <option value="Rscript" selected="true">Rscript</option>
+        <option value="python">python</option>
+        <option value="perl">perl</option>
+        <option value="sh">sh</option>
+    </param>   
+    <param help="The script you are pasting will be run in this image. Make sure it contains the necessary tools" label="Select a docker image" name="docker_image" type="select">
+        <options from_data_table="docker_scriptrunner_images"/>
+    </param>
+    <param name="dynScript" label="Copy and paste the script to be executed here" type="text" value="" area="True" size="8x120"  
+      help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None').">
+      <sanitizer>
+         <valid initial="string.printable">
+         </valid>
+         <mapping initial="none"/>
+      </sanitizer>
+     </param>
+  </inputs>
+  <outputs>
+    <data format_source="input" name="tab_file">
+      <filter>generate_simple_output['make_TAB'] == "yes"</filter>
+        <actions>
+          <action type="format">
+                <option type="from_param" name="generate_simple_output.out_format" />
+          </action>
+        </actions>
+    </data>
+    <data format="html" name="html_file" >
+        <filter>make_HTML == "yes"</filter>
+    </data>
+ </outputs>
+<tests>
+    <test>
+        <param name='input_tab' value='tf2_test_in.xls' ftype='tabular' />
+        <param name="make_TAB" value="yes" />
+        <param name="make_HTML" value="yes" />
+        <param name="out_format" value="tabular" />
+        <param name="interpreter" value='python' />
+        <param name="runme" value="tf2_test_runme.py"/>
+        <output name='output1' file='tf2_test_out.xls' compare='diff' lines_diff = '10'/>
+        <output name='html_file' file="tf2_test.html" compare='diff' lines_diff = '10'/>
+    </test>
+</tests>
+<expand macro="help_macro" />
+<expand macro="test_data_macro" />
+</tool>