--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DimontPredictorWeb.xml	Tue Nov 12 12:55:52 2013 -0500
@@ -0,0 +1,108 @@
+<tool id="DimontPredictor" name="DimontPredictor" version="0.1" force_history_refresh="true">
+<description>for predicting binding sites using a Dimont model</description>
+<command>java -Xms256M -Xmx2G -jar \$JAR_PATH/DimontPredictorWeb.jar --run $script_file $summary $summary.id $__new_file_path__ $summary.extra_files_path</command>
+<inputs>
+<param type="text" size="40" name="DimontPredictor_jobname" label="Job name" value="" optional="true" help="Please enter a name for your job that should be used in the history (optional)">
+</param>
+<param type="data" format="xml" name="DimontPredictor_ps_Dimont" label="&lt;hr /&gt;Dimont" help="The trained Dimont classifier, i.e. the &quot;Dimont&quot; output of a previous Dimont run." value="" optional="false">
+</param>
+
+<param type="data" format="fasta" name="DimontPredictor_ps_Input_sequences" label="&lt;hr /&gt;Input sequences" help="The input sequences for de-novo motif discovery (can be uploaded using &quot;GetData&quot; -&gt; &quot;Upload File&quot;), annotated FastA format. The required format is described in the help section." value="" optional="false">
+</param>
+
+<param type="text" size="40" name="DimontPredictor_ps_Value_tag" label="Value tag" help="The tag for the value information in the FastA-annotation of the input file" value="" optional="false">
+</param>
+
+<param type="text" size="40" name="DimontPredictor_ps_Weighting_factor" label="Weighting factor" help="The value for weighting the data; either a value between 0 and 1, or a description relative to the standard deviation (e.g. +4sd)" value="0.2" optional="false">
+</param>
+
+<param type="float" name="DimontPredictor_ps_p_value" label="&lt;hr /&gt;p-value" help="The maximum p-value allowed for predicted binding sites" value="0.0010" optional="false">
+<validator type="in_range" min="0.0" max="1.0" message="Value is not in the specified range [0.0, 1.0]."/></param>
+
+</inputs>
+<requirements>
+	<requirement type="set_environment">JAR_PATH</requirement>
+	<requirement type="binary" version=">=1.6">java</requirement>
+</requirements>
+<configfiles>
+<configfile name="script_file">
+&lt;DimontPredictor_ps_Dimont&gt;
+&lt;value&gt;
+${DimontPredictor_ps_Dimont}&lt;/value&gt;
+&lt;extension&gt;
+${DimontPredictor_ps_Dimont.ext}&lt;/extension&gt;
+&lt;/DimontPredictor_ps_Dimont&gt;
+
+&lt;DimontPredictor_ps_Input_sequences&gt;
+&lt;value&gt;
+${DimontPredictor_ps_Input_sequences}&lt;/value&gt;
+&lt;extension&gt;
+${DimontPredictor_ps_Input_sequences.ext}&lt;/extension&gt;
+&lt;/DimontPredictor_ps_Input_sequences&gt;
+
+&lt;DimontPredictor_ps_Value_tag&gt;
+${DimontPredictor_ps_Value_tag}&lt;/DimontPredictor_ps_Value_tag&gt;
+
+&lt;DimontPredictor_ps_Weighting_factor&gt;
+${DimontPredictor_ps_Weighting_factor}&lt;/DimontPredictor_ps_Weighting_factor&gt;
+
+&lt;DimontPredictor_ps_p_value&gt;
+${DimontPredictor_ps_p_value}&lt;/DimontPredictor_ps_p_value&gt;
+
+</configfile>
+</configfiles>
+<outputs>
+<data format="html" name="summary" label="#if str($DimontPredictor_jobname) == '' then $tool.name + ' on ' + $on_string else $DimontPredictor_jobname#">
+</data>
+</outputs>
+<tests>
+ <test>
+ 	<param name="DimontPredictor_jobname" value="Test" />
+	<param name="DimontPredictor_ps_Dimont" value="predictor_test.xml" ftype="xml" />
+	<param name="DimontPredictor_ps_Input_sequences" value="dimont_test.fasta" />
+	<param name="DimontPredictor_ps_Value_tag" label="Value tag" value="maxT" />
+	<param name="DimontPredictor_ps_Weighting_factor" value="0.2" />
+	<param name="DimontPredictor_ps_p_value" value="0.0010" />
+	<output name="summary" file="TestPred/TestPred_html.html" />
+ </test>
+</tests>
+<help>
+**DimontPredictor** allows for predicting binding sites in new data using a previously trained Dimont model. For training a Dimont model see tool "Dimont".
+
+This tool may be useful if you, for instance, want to predict binding sites of a previously discovered motifs in other data sets, or if you want to try different p-values for filtering predictions.
+
+Input sequences must be supplied in an annotated FastA format as a file uploaded by the "Upload File" task in section "Get Data" of Galaxy or generated using the "Dimont Data Extractor" tool.
+In the annotation of each sequence, you need to provide a value that reflects the confidence that this sequence is bound by the factor of interest.
+Such confidences may be peak statistics (e.g., number of fragments under a peak) for ChIP data or signal intensities for PBM data.
+
+For instance, an annotated FastA file for ChIP-exo data could look like::
+	
+	> signal: 515
+	ggccatgtgtatttttttaaatttccac...
+	> signal: 199
+	GGTCCCCTGGGAGGATGGGGACGTGCTG...
+	...
+
+where the confidence for the first two sequences amounts to 515 and 199, respectively.
+The FastA comment may contain additional annotations of the format ``key1 : value1; key2: value2;...``.
+We also provide an example_ input file.
+
+Accordingly, you would need to set the parameter "Value tag" to ``signal`` for this input file.
+
+The parameter "Weighting factor" defines the proportion of sequences that you expect to be bound by the targeted factor with high confidence. For ChIP data, the default value of ``0.2`` typically works well. 
+For PBM data, containing a large number of unspecific probes, this parameter should be set to a lower value, e.g. ``0.01``.
+
+The parameter "p-value" defines a threshold on the p-values of predicted binding sites, and only binding sites with a lower p-value are reported by DimontPredictor.
+The Dimont tool uses a p-value threshold of ``1E-3``, which is also the default value of DimontPredictor.
+
+You can also install this web-application within your local Galaxy server. Instructions can be found at the Dimont_ page of Jstacs. 
+There you can also download a command line version of DimontPredictor.
+
+If you experience problems using DimontPredictor, please contact_ us.
+
+.. _example: http://www.jstacs.de/downloads/dimont-example.fa
+.. _Dimont: http://jstacs.de/index.php/Dimont
+.. _contact: mailto:grau@informatik.uni-halle.de
+</help>
+</tool>
+