diff mdust.xml @ 2:79feb4eb7832 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mdust.xml	Wed Nov 18 10:51:42 2015 -0500
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+<?xml version="1.0"?>
+<tool id="mdust" name="mdust" version="1.0">
+	<description>fast and symmetric DUST implementation to mask low-complexity DNA sequences</description>
+	 <requirements>
+		 <requirement type="package" version="1.0">mdust</requirement>
+	 </requirements>
+	<command interpreter="python">
+		mdust_wrapper.py -i ${input_file} -v ${cutoff} -w ${wsize} -m ${masking_letter.masking_letter_selector} -f ${output_type.output_type_selector}
+		
+		#if str( $output_type.output_type_selector) == "default"
+			-o ${output_masked_fasta}
+		#end if
+
+		#if str( $output_type.output_type_selector) == "tab"
+			-o ${output_tab}
+		#end if
+
+		#if str( $output_type.output_type_selector) == "bed"
+			-o ${output_bed}
+		#end if
+	</command>
+	<inputs>
+		<param name="input_file" type="data" format="fasta" label="Input fasta file" help=""/>
+		<param name="cutoff" type="integer" value="28" label="cutt-off" help="cut-off" />
+		<param name="wsize" type="integer" value="3" label="set maximum word size" help="word-size" />
+		<conditional name="masking_letter">
+			<param name="masking_letter_selector" type="select" label="Choose your masking type" help="Select the masking letter (N,X or lowercase)" >
+				<option value="N" selected="True">N (default)</option>
+				<option value="X">X</option>
+				<option value="L">lowercase</option>
+			</param>
+		</conditional>
+		<conditional name="output_type">
+			<param name="output_type_selector" type="select" label="Choose your output type" help="select your output">
+				<option value="default" selected="True">masked file (default)</option>
+				<option value="tab">output masking coordinates only (tab delimited)</option>
+				<option value="bed">output masking coordinates only (bed format)</option>
+			</param>
+		</conditional>
+	</inputs>
+	<outputs>
+		<data format="fasta" name="output_masked_fasta" label="masked.${input_file.name}">
+			<filter>( output_type['output_type_selector'] == 'default' )</filter>
+		</data>
+		<data format="tabular" name="output_tab" label="${input_file.name}.tab">
+			<filter>( output_type['output_type_selector'] == 'tab' )</filter>
+		</data>
+		<data format="bed" name="output_bed" label="${input_file.name}.bed">
+			<filter>( output_type['output_type_selector'] == 'bed' )</filter>
+		</data>
+	</outputs>
+	<tests>
+		<test>
+			<param name="input_file" value="seq-mdust.fsa" />
+			<output name="output_masked_fasta" file="masked-seq-mdust.fsa" ftype="fasta" />
+		</test>
+	</tests>
+	 <help><![CDATA[
+mdust new implementation of the DUST module that uses the same function to assign a complexity score to a sequence, but uses a different rule by which high-scoring sequences are masked.
+
+-----
+
+**Usage:** ::
+
+	mdust [<fasta-file>] [-w <wsize>] [-v <cut-off>] [-m N|X|L] [-c] 
+	  if no <fasta-file> is given, a multi-fasta stream is expected at stdin
+	  -v default <cut-off> value is 28 (lower values might mask more, 
+	  but possibly still useful sequence; > 64 will rarely mask poly-triplets)
+	  -w set maximum word size to <wsize> (default 3)
+	  -m if fasta output is not disabled by -c, set the masking letter type:
+	     N ('N', default), X ('X'), L (make lowercase)
+	  -c output masking coordinates only: 
+	     seq_name, seqlength, mask_start, mask_end  (tab delimited)
+
+-----
+
+**Reference:** ::
+
+  A fast and symmetric DUST implementation to mask low-complexity DNA sequences.
+  Morgulis A, Gertz EM, Schäffer AA, Agarwala R.
+  J Comput Biol. 2006 Jun;13(5):1028-40.
+  PMID:16796549
+
+
+]]>
+	</help>	 
+</tool>