--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyExtractLinesFromGTF.xml	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,77 @@
+ <tool id ="pyExtractLinesFromGTF" name="pyExtractLinesFromGTF">
+	<requirements>
+        	<requirement type="package">pyCRAC</requirement>
+    	</requirements>
+	<command interpreter="python"> 
+	/usr/local/bin/pyExtractLinesFromGTF.py --gtf $addGTF.gtf --genes_file $g --attribute $attribute $v -o $out
+	</command>
+	<version_command>/usr/local/bin/pyExtractLinesFromGTF.py --version</version_command>
+	<inputs>
+		<conditional name="addGTF">
+			<param name="gtfFile" type="select"  label="Choose GTF File from">
+				<option value="default" selected="true">Defaults</option>
+				<option value="other">History</option>
+			</param>	
+			<when value="default">
+				<param name="gtf" type="select"  label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
+					<options from_data_table="pycrac_gtf"/>
+				</param>
+			</when>
+			<when value="other">
+				<param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
+			</when>
+		</conditional>
+		<param format="txt" name="g" type="data" label="File containing gene list --genes_file" help="Tabular file with 1 column of gene or annotation names"/>
+		<param name="attribute" type="select"  label="Select the attribute to extract names from --attribute">
+                                <option value="gene_name" selected="true">gene_name</option>
+                                <option value="gene_id">gene_id</option>
+                                <option value="transcript_name">transcript_name</option>
+                                <option value="transcript_id">transcript_id</option>
+		</param>
+                <param name="v" type="select"  label="Extract lines from GTF that -v">
+                                <option value="" selected="true">Match the gene file</option>
+                                <option value="-v">Do not match in gene fil</option>
+                </param>
+		<param name="label" type="text" format="txt" size="30" value="pyExtractLinesFromGTF" label="Enter output file label -o" />
+	</inputs>
+
+	<outputs>
+		<data format="gtf" name="out" label="${label.value}.gtf"/>
+	</outputs>
+	<help>
+.. class:: infomark
+
+**pyExtractLinesFromGTF**
+
+pyExtractLinesFromGTF is part of the pyCRAC_ package. Extracts lines from a GTF file that contain gene names of interest.
+
+
+.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
+        
+------
+
+**Parameter list**
+
+Options::
+
+  --gtf=Yourfavoritegtf.gtf
+                        type the path to the gtf file that you want to use. By
+                        default it expects data from the standard input.
+  -g FILE, --genes_file=FILE
+                        name of your gene list or annotations list file (1
+                        column)
+  -o OUTFILE, --outfile=OUTFILE
+                        type the name and path of the file you want to write
+                        the output to. Default is standard output
+  -a ATTRIBUTE, --attribute=ATTRIBUTE
+                        from which attribute do you want to extract names?
+                        Choices: gene_name, gene_id, transcript_name,
+                        transcript_id
+  -v                    
+                        similar to grep -v option. Remove the genes from the
+                        GTF that are in the gene list
+
+
+
+	</help>
+</tool>