Mercurial > repos > grau > dimont_deprecated
diff DimontPredictorWeb.xml @ 0:5130880b8e0a draft
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author | grau |
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date | Tue, 12 Nov 2013 12:55:52 -0500 |
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--- /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__ $summary.extra_files_path</command> +<inputs> +<param type="text" size="40" name="DimontPredictor_jobname" label="Job name" value="" optional="true" help="Please enter a name for your job that should be used in the history (optional)"> +</param> +<param type="data" format="xml" name="DimontPredictor_ps_Dimont" label="<hr />Dimont" help="The trained Dimont classifier, i.e. the "Dimont" output of a previous Dimont run." value="" optional="false"> +</param> + +<param type="data" format="fasta" name="DimontPredictor_ps_Input_sequences" label="<hr />Input sequences" help="The input sequences for de-novo motif discovery (can be uploaded using "GetData" -> "Upload File"), annotated FastA format. The required format is described in the help section." value="" optional="false"> +</param> + +<param type="text" size="40" name="DimontPredictor_ps_Value_tag" label="Value tag" help="The tag for the value information in the FastA-annotation of the input file" value="" optional="false"> +</param> + +<param type="text" size="40" name="DimontPredictor_ps_Weighting_factor" label="Weighting factor" help="The value for weighting the data; either a value between 0 and 1, or a description relative to the standard deviation (e.g. +4sd)" value="0.2" optional="false"> +</param> + +<param type="float" name="DimontPredictor_ps_p_value" label="<hr />p-value" help="The maximum p-value allowed for predicted binding sites" value="0.0010" optional="false"> +<validator type="in_range" min="0.0" max="1.0" message="Value is not in the specified range [0.0, 1.0]."/></param> + +</inputs> +<requirements> + <requirement type="set_environment">JAR_PATH</requirement> + <requirement type="binary" version=">=1.6">java</requirement> +</requirements> +<configfiles> +<configfile name="script_file"> +<DimontPredictor_ps_Dimont> +<value> +${DimontPredictor_ps_Dimont}</value> +<extension> +${DimontPredictor_ps_Dimont.ext}</extension> +</DimontPredictor_ps_Dimont> + +<DimontPredictor_ps_Input_sequences> +<value> +${DimontPredictor_ps_Input_sequences}</value> +<extension> +${DimontPredictor_ps_Input_sequences.ext}</extension> +</DimontPredictor_ps_Input_sequences> + +<DimontPredictor_ps_Value_tag> +${DimontPredictor_ps_Value_tag}</DimontPredictor_ps_Value_tag> + +<DimontPredictor_ps_Weighting_factor> +${DimontPredictor_ps_Weighting_factor}</DimontPredictor_ps_Weighting_factor> + +<DimontPredictor_ps_p_value> +${DimontPredictor_ps_p_value}</DimontPredictor_ps_p_value> + +</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> +