# HG changeset patch
# User da-intersect
# Date 1365577261 14400
# Node ID e49ba3299767d7099f68425dfa601782ed410afd
# Parent  13e3de4582604eff5e93d05cfcd8f97f7a165388
Uploaded

diff -r 13e3de458260 -r e49ba3299767 protein_generator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_generator.xml	Wed Apr 10 03:01:01 2013 -0400
@@ -0,0 +1,56 @@
+<tool id="protgenerator" name="Protein Generator" version="0.0.1">
+        <description>Protein Generator</description>
+        <command interpreter="bash">
+       	protein_generator.sh protein_generator.jar 
+        -d "$databasename" 
+        -f "$genomeFile" 
+        #if $GlimmerFile
+        	-g "$GlimmerFile"
+        #end if
+        #if $SplitInterval
+        	-i "$SplitInterval"
+        #end if
+        	-o "$output1"
+        #if $condition1.gffFile == "yes"
+		-p "$output2"
+	#end if
+	#if $condition2.accessionFile == "yes"
+		-q "$output3"
+	#end if
+	#if $trans_tab_file
+		-t "$trans_tab_file"
+	#end if
+        </command>
+        <inputs>
+        	<param name="databasename" type="text" label="Database name" />
+        	<param name="genomeFile" type="data" format="faa" label="Select genome file" help="Genome file in gff format" />
+
+        	<param name="GlimmerFile" type="data" format="txt" label="Select Glimmer File" help="Glimmer txt file. Can't be used with the Split Interval" optional="true" />
+		<param name="SplitInterval" type="integer" label="Size of the intervals" help="Size of the intervals (number of codons) into which the genome will be split. Can't be used with the Glimmer File" optional="true" />
+
+		<param name="trans_tab_file" type="data" format="txt" label="Select Translation Table File" help="File containing a mapping of codons to amino acids, in the format used by NCBI." optional="true" />
+		<conditional name="condition1">
+			<param name="gffFile" type="select" help="write the GFF file">
+				<option value="yes" selected="True">Yes</option>
+				<option value="no" selected="False">No</option>
+			</param>
+		</conditional>
+		<conditional name="condition2">
+			<param name="accessionFile" type="select" label="Accession File" help="Write the accession file">
+				<option value="yes" selected="True">Yes</option>
+				<option value="no" selected="False">No</option>
+			</param>
+		</conditional>
+	</inputs>
+        <outputs>
+                <data format="sam" name="output1" />
+		<data format="gff" name="output2" label="GFF file">
+			<filter>condition1['gffFile'] == "yes"</filter>
+		</data>
+                <data format="txt" name="output3" label="Accession File">
+                	<filter>condition2['accessionFile'] == "yes"</filter>
+                </data>
+        </outputs>
+        <help>
+        </help>
+</tool>