annotate DimontDataExtractor.xml @ 0:b7d6db3ba6bc draft

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<tool id="DimontDataExtractor" name="Dimont Data Extractor" version="0.1">
<description>prepares data in the format required by Dimont</description>
<command interpreter="perl">extract_data_single_galaxy.pl $genomefa $regions $chromcol $startcol $seccol $seccoord $width $statcol $extracted</command>
<inputs>
	<param type="data" format="bed,gtf,txt,tabular" name="regions" label="Genomic regions" value="" optional="false" help="The genomic regions to be extracted in a BED-like file format, e.g., BED, GTF, narrowPeak." />
	<param type="data" format="fasta" name="genomefa" label="Genome sequence" value="" optional="false" help="The input genome to which the genomic regions refer." />
	<param type="data_column" data_ref="regions" force_select="true" name="chromcol" label="Chromosome column" value="1" optional="false" help="The column of the regions file, which contains the chromosome information." />
	<param type="data_column" data_ref="regions" force_select="true" name="startcol" label="Start column" value="2" optional="false" help="The column of the Regions file containing the start position of the genomic region." />
	<param type="select" name="seccol" label="Meaning of second coordinate" optional="false" help="The meaning of the second genomic coordinate. This may either be the position of the peak summit relative to the position in Start, or the end position of the peak.">
		<option value="end">End of peak (in global coordinates)</option>
		<option value="center">Center of peak (relative to start)</option>
	</param>
	<param type="data_column" data_ref="regions" force_select="true" name="seccoord" label="Second coordinate" value="3" optional="false" help="The second genomic coordinate with meaning specified by parameter &quot;Meaning of second coordinate&quot;" />
	<param type="data_column" data_ref="regions" force_select="true" name="statcol" label="Statistics column" value="7" optional="false" help="The column containing the peak statistics information (or another measure of peak confidence)." />
	<param type="integer" name="width" label="Width" value="1000" optional="false" help="The width of the genomic region to be extracted. Recommended values: 1000 for ChIP-seq and 100 for ChIP-exo." />
</inputs>
<outputs>
	<data format="fasta" name="extracted">
	</data>
</outputs>
<tests>
	<test>
		<param name="regions" value="mini.bed" />
		<param name="genomefa" value="minigenome.fa" />
		<param name="chromcol" value="1" />
		<param name="startcol" value="2" />
		<param name="seccol" value="end" />
		<param name="seccoord" value="3" />
		<param name="statcol" value="7" />
		<param name="width" value="200" />
		<output name="extracted" file="mini_extracted.fa" /> 
	</test>
	<test>
		<param name="regions" value="mini2.bed" />
		<param name="genomefa" value="minigenome.fa" />
		<param name="chromcol" value="1" />
		<param name="startcol" value="2" />
		<param name="seccol" value="center" />
		<param name="seccoord" value="3" />
		<param name="statcol" value="7" />
		<param name="width" value="200" />
		<output name="extracted" file="mini2_extracted.fa" /> 
	</test>
</tests>
<help>
**Dimont Data Extractor** prepares an annotated FastA file as required by Dimont from a genome (in FastA format) and a tabular file (e.g., BED, GTF, narrowPeak,...). The regions specified in the tabular file are used to determine the center of the extracted sequences. All extracted sequences have the same length as specified by parameter "Width".

In case of ChIP data, the center position could for instance be the peak summit.
An annotated FastA file for ChIP-exo data comprising sequences of length 100 centered around the peak summit might look like::
	
	> peak: 50; signal: 515
	ggccatgtgtatttttttaaatttccac...
	> peak: 50; signal: 199
	GGTCCCCTGGGAGGATGGGGACGTGCTG...
	...

where the center is given as 50 for the first two sequences, and the confidence amounts to 515 and 199, respectively.

We also provide an example_ input file and a stand alone Perl script_ for preparing data in the format required by Dimont_.


If you experience problems using Dimont Data Extractor, please contact_ us.

.. _example: http://www.jstacs.de/downloads/dimont-example.fa
.. _script: http://www.jstacs.de/index.php/Dimont#Data_preparation
.. _Dimont: http://jstacs.de/index.php/Dimont
.. _contact: mailto:[e-mail]
</help>
</tool>