# HG changeset patch
# User da-intersect
# Date 1365576062 14400
# Node ID 795f289b64dbc84a593f33b1e3facc03459c581d
# Parent  1f62ceeae7a19e69ef162593fd9c417d081c9111
First complete upload, containing the datatype TAR.

diff -r 1f62ceeae7a1 -r 795f289b64db datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<datatypes>
+	<datatype_files>
+		<datatype_file name="tar.py"/>
+	</datatype_files>
+	<registration>
+		<datatype extension="tar" type="galaxy.datatypes.tar:Tar"/>
+	<registration>
+</datatypes>
diff -r 1f62ceeae7a1 -r 795f289b64db jars/codon_finder.jar
Binary file jars/codon_finder.jar has changed
diff -r 1f62ceeae7a1 -r 795f289b64db jars/nucleotide_to_amino_acid.jar
Binary file jars/nucleotide_to_amino_acid.jar has changed
diff -r 1f62ceeae7a1 -r 795f289b64db jars/protein_generator.jar
Binary file jars/protein_generator.jar has changed
diff -r 1f62ceeae7a1 -r 795f289b64db jars/results_analyser.jar
Binary file jars/results_analyser.jar has changed
diff -r 1f62ceeae7a1 -r 795f289b64db jars/samifier.jar
Binary file jars/samifier.jar has changed
diff -r 1f62ceeae7a1 -r 795f289b64db jars/virtual_protein_merger.jar
Binary file jars/virtual_protein_merger.jar has changed
diff -r 1f62ceeae7a1 -r 795f289b64db protein_generator.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_generator.sh	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,31 @@
+#!/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 [ $# -eq 0 ]
+then
+  echo "USAGE ap11Runner.sh APPNAME [ARGS]";
+  exit;
+fi
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+jar_path="${DIR}/jars/${1}"
+shift
+
+java -jar $jar_path $@
diff -r 1f62ceeae7a1 -r 795f289b64db protein_generator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_generator.xml	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,56 @@
+<tool id="protgenerator" name="Protein Generator" version="0.0.1">
+        <description>Protein Generator</description>
+        <command interpreter="bash">
+       	protein_generator.sh protein_generator.jar 
+        -d "$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>
diff -r 1f62ceeae7a1 -r 795f289b64db protein_merger.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_merger.sh	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,38 @@
+#!/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 [ $# -eq 0 ]
+then
+  echo "USAGE ap11Runner.sh APPNAME [ARGS]";
+  exit;
+fi
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+jar_path="${DIR}/jars/${1}"
+shift
+tar_file="$1"
+shift
+temp_dir=$(basename "$tar_file")
+
+mkdir -p /tmp/$temp_dir
+
+tar -C /tmp/$temp_dir -xvf $tar_file
+java -jar $jar_path $@ -c "/tmp/$temp_dir"
+rm -rf "/tmp/$temp_dir"
diff -r 1f62ceeae7a1 -r 795f289b64db protein_merger.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_merger.xml	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,21 @@
+<tool id="protmerger" name="Protein Merger" version="0.0.1">
+        <description>Virtual Protein Merger</description>
+        <command interpreter="bash">
+        protein_merger.sh virtual_protein_merger.jar -g "$genomeFile" -o "$output1" 
+        -r "$searchResultsFile" 
+	#if $trans_tab_file
+	-t "$trans_tab_file"
+	#end if
+        </command>
+        <inputs>
+        	<param name="genomeFile" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
+        	<param name="searchResultsFile" type="data" format="txt" label="Select Mascot search result" help="Mascot search results file in txt format" />
+		<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"/>
+
+	</inputs>
+        <outputs>
+                <data format="sam" name="output1" />
+        </outputs>
+        <help>
+        </help>
+</tool>
diff -r 1f62ceeae7a1 -r 795f289b64db result_analyser.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/result_analyser.sh	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,39 @@
+#!/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 [ $# -eq 0 ]
+then
+  echo "USAGE ap11Runner.sh APPNAME [ARGS]";
+  exit;
+fi
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+jar_path="${DIR}/jars/${1}"
+chr_path="${DIR}/chromosome"
+shift
+tar_file="$1"
+shift
+temp_dir=$(basename "$tar_file")
+
+mkdir -p /tmp/$temp_dir
+
+tar -C /tmp/$temp_dir -xvf $tar_file
+java -jar $jar_path $@ -c "/tmp/$temp_dir"
+rm -rf "/tmp/$temp_dir"
diff -r 1f62ceeae7a1 -r 795f289b64db result_analyser.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/result_analyser.xml	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,30 @@
+<tool id="resanalyser" name="Result Analyser" version="0.0.1">
+        <description>Result Analyser</description>
+        <command interpreter="bash">
+        result_analyser.sh results_analyser.jar -g "$genomeFile" -m "$mapping" -o "$output1" -r "$searchResultsFile" 
+        #if $reportId
+        -rep "$reportId"
+        #end if
+        #if $reportList
+        -replist "$reportList"
+        #end if
+        #if $sqlQuery
+        -sql "$sqlQuery"
+        #end if
+        </command>
+        <inputs>
+        	<param name="genomeFile" type="data" format="gff" label="Select genome file" help="Genome file in gff format" />
+        	<param name="searchResultsFile" 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="reportId" optional="true" type="data" format="txt" label="Select reportId" help="Access a built in report query" />
+		<param name="reportList" optional="true" type="data" format="txt" label="Select reportList" help="A file containing all the pre-built SQL queries" />
+		<param name="sqlQuery" optional="true" type="data" format="txt" label="Select SQL Query" help="Filters the result through the use of a SQL statement to the output file" />
+
+	</inputs>
+        <outputs>
+                <data format="sam" name="output1" />
+        </outputs>
+        <help>
+        </help>
+</tool>
diff -r 1f62ceeae7a1 -r 795f289b64db samifier.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier.sh	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,39 @@
+#!/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 [ $# -eq 0 ]
+then
+  echo "USAGE ap11Runner.sh APPNAME [ARGS]";
+  exit;
+fi
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+jar_path="${DIR}/jars/${1}"
+chr_path="${DIR}/chromosome"
+shift
+tar_file="$1"
+shift
+temp_dir=$(basename "$tar_file")
+
+mkdir -p /tmp/$temp_dir
+
+tar -C /tmp/$temp_dir -xvf $tar_file
+java -jar $jar_path $@ -c "/tmp/$temp_dir"
+rm -rf "/tmp/$temp_dir"
diff -r 1f62ceeae7a1 -r 795f289b64db samifier.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier.xml	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,46 @@
+<tool id="samifier" name="Samifier" version="1.0.0">
+        <description>Samifier vX.X</description>
+        <command interpreter="bash">
+        samifier.sh samifier.jar $chromosome_tar -g "$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="chromosome_tar" type="data" format="tar" label="Select chromosome zip files" help="A zip file containing all the chromosome files" />
+        	<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>
diff -r 1f62ceeae7a1 -r 795f289b64db tar.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tar.py	Wed Apr 10 02:41:02 2013 -0400
@@ -0,0 +1,34 @@
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+
+import logging, os, sys, time, sets, tempfile, shutil
+import data
+from galaxy import util
+from galaxy.datatypes.sniff import *
+from galaxy.datatypes.binary import Binary
+import tarfile
+
+class Tar( Binary ):
+    """Class describing a BAM binary file"""
+    file_ext = "tar"
+    def sniff( self, filename ):
+        try:
+            if tarfile.is_tarfile(filename):
+                return True
+            return False
+        except:
+            return False
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek  = "Tar file"
+            dataset.blurb = data.nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+    def display_peek( self, dataset ):
+        try:
+            return dataset.peek
+        except:
+            return "Tar file (%s)" % ( data.nice_size( dataset.get_size() ) )
+