--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_fasta_validator.xml	Wed Jan 08 11:34:51 2014 +0100
@@ -0,0 +1,42 @@
+<tool name="Fasta Validator" id="masscomb_fastavalidator" version="1.0.1">
+	<description>Basic FASTA file validation</description>
+	<!-- 
+	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
+	       java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 
+	-->    
+	<command interpreter="java -jar">
+	    MassComb.jar 
+	    -action FASTAVALIDATOR 
+	    -fastaFile $inputFile 
+	    -outputFile $outputFile 
+	    -expressions "$expressions"
+	    -maxLengthSequenceLine $maxLengthSequenceLine
+	    </command>
+<inputs>
+	<param name="inputFile" type="data" format="" label="Fasta file to validate"/>
+    
+	<param name="expressions" type="select" display="checkboxes" multiple="true" label="Error patterns to search for in each line" help="">
+      	<option value="description=White space in SEQUENCE;regex=^[a-zA-Z]+SLASHs[a-zA-Z]">White space in SEQUENCE (^[a-zA-Z]+\s[a-zA-Z])</option>
+      	<option value="description=Numbers in SEQUENCE;regex=^[0-9]PIPE^[a-zA-Z]+.*[0-9]">Numbers in SEQUENCE (^[0-9]|^[a-zA-Z]+.*[0-9])</option>
+      	<option value="description=Line starting with white space followed by alpha numeric characters;regex=^SLASHs[a-zA-Z0-9]+">Line starting with white space followed by alpha numeric characters (^\s[a-zA-Z0-9]+)</option>
+      	<option value="description=Line ending with white space;regex=.*SLASHsDOLLAR">Line ending with white space (.*\s$)</option>
+      	<option value="description=Sequence lines with non-Amino Acid characters;regex=(^[SLASHwAMPAMP[^ARNDCEQGHILKMFPSTWYV]])PIPE(^[ARNDCEQGHILKMFPSTWYV]+[SLASHwAMPAMP[^ARNDCEQGHILKMFPSTWYV]]+)">Sequence lines with non-Amino Acid characters ((^[\w&amp;&amp;[^ARNDCEQGHILKMFPSTWYV]])|(^[ARNDCEQGHILKMFPSTWYV]+[\w&amp;&amp;[^ARNDCEQGHILKMFPSTWYV]]+))</option>
+      	<option value="description=Hyphen in accession numbers;regex=^SLASHS*-">Hyphen in accession numbers (^\S*-)</option>
+      	<option value="description=Lines with stretches of X;regex=XX+">Lines with stretches of X (XX+)</option>
+    </param>
+
+	<param name="maxLengthSequenceLine" type="integer" size="10" value="0" label="Max length sequence line " 
+	help="(Optional) the maximum line width in the protein sequence part. Leave to 0 (zero) for no restrictions "/>
+
+</inputs>
+<outputs>
+	<data format="txt" name="outputFile" />
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+</help>
+</tool>