# HG changeset patch
# User da-intersect
# Date 1365468648 14400
# Node ID 5f91d3a4d18c8de9926292fa0a1d5d68c452a4e6
# Parent  9f555d1f63b5d2525abcceb53c2cbd8390ede0e1
Deleted selected files

diff -r 9f555d1f63b5 -r 5f91d3a4d18c javaRunner.sh
--- a/javaRunner.sh	Mon Apr 08 20:49:59 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#!/bin/bash
-
-if (type -p java >> /dev/null); then
-    _java=java
-elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then
-    _java="$JAVA_HOME/bin/java"
-else
-    echo "You must install java before runing this tool"
-    exit 1
-fi
-
-if [[ "$_java" ]]; then
-    version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
-    if ! [[ "$version" > "1.6" ]]; then
-        echo "Java version should be > 1.6"
-	exit 1
-    fi
-fi
-
-if [ $# -eq 0 ]
-then
-  echo "USAGE ap11Runner.sh APPNAME [ARGS]";
-  exit;
-fi
-
-jar_path="/usr/local/galaxy-dist/tools/ap11/jars/$1"
-shift
-
-java -jar $jar_path $@
diff -r 9f555d1f63b5 -r 5f91d3a4d18c samifier.xml
--- a/samifier.xml	Mon Apr 08 20:49:59 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-<tool id="samifier" name="Samifier" version="1.0.0">
-        <description>Samifier vX.X</description>
-        <command interpreter="bash">
-        javaRunner.sh samifier.jar -c "/usr/local/galaxy-dist/tools/ap11/chromosome/" -g "$genome" -m "$mapping" -o "$output1" -r "$mascot"
-	#if $score_thresold
-	-s "$score_thresold"
-	#end if
-	#if $condition2.tool_option2 == "yes"
-	-l "$output2"
-	#end if
-	#if $condition3.tool_option3 == "yes"
-	-b "$output3"
-	#end if
-        </command>
-        <inputs>
-        	<param name="genome" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
-        	<param name="mascot" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
-        	<param name="mapping" type="data" format="txt" label="Select file mapping" help="File mapping protein identifier to ordered locus name" />
-		<param name="score_thresold"  type="integer" label="Confidence Score thresold" help="Minimum confidence score for peptides to" optional="true"/>
-
-		<conditional name="condition2">
-			<param name="tool_option2" type="select" label="Write log file" help="Create an output containing the logs">
-				<option value="yes" selected="No">Yes</option>
-				<option value="no" selected="Yes">No</option>
-			</param>
-		</conditional>
-		<conditional name="condition3">
-			<param name="tool_option3" type="select" label="Write output in bed format" help="Output to write IGV regions of interest">
-				<option value="yes" selected="No">Yes</option>
-				<option value="no" selected="Yes">No</option>
-        		</param>
-        	</conditional>
-        </inputs>
-        <outputs>
-                <data format="sam" name="output1" />
-                <data format="txt" name="output2" label="Samifier log file">
-                	<filter>condition2['tool_option2'] == "yes"</filter>
-                </data>
-                <data format="bed" name="output3" label="Samifier Bed">
-                	<filter>condition3['tool_option3'] == "yes"</filter>
-                </data>
-        </outputs>
-        <help>
-        </help>
-</tool>