changeset 14:7e29033239c8 draft

Deleted selected files

--- a/datatypes_conf.xml	Wed Apr 10 03:05:25 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <datatype_files>
-    <datatype_file name="tar.py"/>
-  </datatype_files>
-  <registration>
-    <datatype extension="tar" type="galaxy.datatypes.tar:Tar" display_in_upload="true"/>
-  </registration>
-  <sniffers>
-    <sniffer type="galaxy.datatypes.tar:Tar"/>
-  </sniffers>
-</datatypes>
\ No newline at end of file

--- a/protein_generator.xml	Wed Apr 10 03:05:25 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<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>