comparison DimontWeb.xml @ 11:fa520092c603 draft

Uploaded

10:247f7edbe7f8

<tool id="Dimont" name="Dimont" version="0.1" force_history_refresh="true">
<description>Dimont, a universal tool for de-novo motif discovery (beta).</description>
<command>java -Xms256M -Xmx2G -jar \$JAR_PATH/DimontWeb.jar --run $script_file $summary $summary.id $__new_file_path__ $summary.extra_files_path</command>
<inputs>
<param type="text" size="40" name="Dimont_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="fasta" name="Dimont_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">

	</test>
</tests>
<help>
**Dimont** is a universal tool for de-novo motif discovery. Dimont has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.

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.
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. In addition, you need to provide an anchor position within the sequence. 
In case of ChIP data, this anchor position could for instance be the peak summit.
For instance, an annotated FastA file for ChIP-exo data comprising sequences of length 100 centered around the peak summit could look like::
	

11:fa520092c603

<tool id="Dimont" name="Dimont" version="0.1" force_history_refresh="true">
<description>Dimont, a universal tool for de-novo motif discovery.</description>
<command>java -Xms256M -Xmx2G -jar \$JAR_PATH/DimontWeb.jar --run $script_file $summary $summary.id $__new_file_path__ $summary.extra_files_path</command>
<inputs>
<param type="text" size="40" name="Dimont_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="fasta" name="Dimont_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">

	</test>
</tests>
<help>
**Dimont** is a universal tool for de-novo motif discovery. Dimont has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.

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. In addition, you need to provide an anchor position within the sequence. 
In case of ChIP data, this anchor position could for instance be the peak summit.
For instance, an annotated FastA file for ChIP-exo data comprising sequences of length 100 centered around the peak summit could look like::