--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DockerToolFactory.xml	Sat Oct 03 08:34:39 2015 -0400
@@ -0,0 +1,206 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<tool id="rgTF" name="docker_tool_factory" version="0.1.3">
+    <description>Makes scripts into tools using Docker</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="9.10">ghostscript</requirement>
+        <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+        <requirement type="package" version="0.4.0">docker-py</requirement>
+    </requirements>
+    <command interpreter="python"><![CDATA[
+        DockerToolFactory.py --script_path "$runme" --interpreter "$interpreter"
+        --tool_name "$tool_name" --user_email "$__user_email__"
+        #if $generate_simple_output.make_TAB=="yes":
+        --output_tab "$tab_file"
+        #end if
+        #if $makeMode.make_Tool=="yes":
+        #if generate_simple_output.make_TAB=="yes":
+        --output_format "$out_format"
+        #end if
+        --make_Tool "$makeMode.make_Tool"
+        --tool_desc "$makeMode.tool_desc"
+        --tool_version "$makeMode.tool_version"
+        --new_tool "$new_tool"
+        --help_text "$helpme"
+        #if $make_HTML.value=="yes":
+        --include_dependencies "${makeMode.include_deps}"
+        #end if
+        #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 $input_files:
+        --input_format
+        #if str($i.in_format) == "None":
+        "Any"
+        #else
+        "$i.in_format"
+        #end if
+        #end for
+        #end if
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="runme">$dynScript</configfile>
+        <configfile name="helpme">
+            #if $makeMode.make_Tool == "yes":
+            ${makeMode.help_text}
+            #end if
+        </configfile>
+    </configfiles>
+    <inputs>
+        <repeat name="input_files" title="Select input files">
+            help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
+            <param name="in_format" type="select" optional="true" multiple="true"
+                   label="Optional: Select the allowed input datatype(s) for your tool/script">
+                <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+                    <column name="value" index="0"/>
+                </options>
+            </param>
+        </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="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs"
+               size="60"
+               help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
+            <sanitizer invalid_char="">
+                <valid initial="string.printable"/>
+            </sanitizer>
+        </param>
+        <conditional name="makeMode">
+            <param name="make_Tool" type="select" label="Create a tar.gz file ready for local toolshed entry"
+                   help="Ready to deploy securely!" size="60">
+                <option value="yes">Generate a Galaxy ToolShed compatible toolshed.gz</option>
+                <option value="" selected="true">No. Just run the script please</option>
+            </param>
+            <when value="yes">
+                <param name="tool_version" label="Tool Version - bump this to warn users trying to redo old analyses"
+                       type="text" value="0.01"
+                       help="If you change your script and regenerate the 'same' tool, you should inform Galaxy (and users) by changing (bumping is traditional) this number"/>
+                <param name="tool_desc" label="Tool Description" type="text" value="" size="40"
+                       help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)"/>
+                <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
+                       size="8x120" value="**What it Does**"
+                       help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                        </valid>
+                        <mapping initial="none"/>
+                    </sanitizer>
+                </param>
+                <param name="include_deps" type="select"
+                       label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
+                       help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
+                    <option value="">Rely on system ghostscript and graphicsmagick rather than include these as
+                        dependencies
+                    </option>
+                    <option value="yes" selected="true">Include dependencies so target installations will always work if
+                        HTML is being generated
+                    </option>
+                </param>
+
+            </when>
+            <when value="">
+            </when>
+        </conditional>
+        <param name="out_format" type="text" value="txt" hidden="True"/>
+        <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="no">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" optional="True">
+                    <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
+                        <column name="value" index="0"/>
+                    </options>
+                </param>
+            </when>
+            <when value="no">
+                 <param name="out_format" type="text" value="txt" optional="True" hidden="True"/>
+            </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 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" label="${tool_name}.${out_format}"> -->
+        <data format_source="input" name="tab_file">
+            <filter>generate_simple_output['make_TAB'] == "yes"</filter>
+            <actions>
+                <action type="format">
+                    <option type="from_param" name="out_format"/>
+                </action>
+            </actions>
+        </data>
+        <data format="html" name="html_file" label="${tool_name}.html">
+            <filter>make_HTML == "yes"</filter>
+        </data>
+        <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
+            <filter>makeMode['make_Tool'] == "yes"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="interpreter" value="Rscript"/>
+            <param name="make_HTML" value="yes"/>
+            <param name="generate_simple_output|makeTAB" value="no"/>
+            <param name="out_format" value="txt"/>
+	    <param name="dynScript" value="for (i in 1:10) {; foo = runif(100); bar = rnorm(100); bar = foo + bar; pdf(&quot;anotherplot.pdf&quot;); plot(1,2); dev.off();}"/>
+            <output name="html_file" file="html_output/My_dynamic_script_html.html" compare="diff"/>
+        </test>
+    </tests>
+    <expand macro="help_macro"/>
+</tool>