# HG changeset patch
# User marc-wilkins
# Date 1375836204 14400
# Node ID 66ad014e6975f2e41062f6f76725e43e462e31f7
# Parent  afa0439120d88010915b86280e504afe80c23fa4
Uploaded

diff -r afa0439120d8 -r 66ad014e6975 samifier/datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/datatypes_conf.xml	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,12 @@
+<?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
diff -r afa0439120d8 -r 66ad014e6975 samifier/protein_generator.jar
Binary file samifier/protein_generator.jar has changed
diff -r afa0439120d8 -r 66ad014e6975 samifier/protein_generator.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/protein_generator.sh	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+if (type -p java >> /dev/null); then
+    _java=java
+elif [[ -n "$JAVA_HOME" ]] && [[ -x "$JAVA_HOME/bin/java" ]];  then
+    _java="$JAVA_HOME/bin/java"
+else
+    echo "You must install java before runing this tool" >&2
+    exit 1
+fi
+
+if [[ "$_java" ]]; then
+    version=$("$_java" -version 2>&1 | awk -F '"' '/version/ {print $2}')
+    if ! [[ "$version" > "1.6" ]]; then
+        echo "Java version should be > 1.6" >&2
+	exit 1
+    fi
+fi
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+jar_path="${DIR}/${1}"
+shift
+
+java -Xmx3072M -jar $jar_path $@
diff -r afa0439120d8 -r 66ad014e6975 samifier/protein_generator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/protein_generator.xml	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,56 @@
+<tool id="protgenerator" name="Protein Generator" version="1.0.9">
+        <description>Protein Generator</description>
+        <command interpreter="bash">
+       	protein_generator.sh protein_generator.jar 
+        -d "$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 afa0439120d8 -r 66ad014e6975 samifier/protein_merger.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/protein_merger.sh	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# Check java version
+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
+
+# Locate the jar directory
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+jar_path="${DIR}/${1}"
+shift
+
+# Untar the chromosome file into a temporary directory
+tar_file="$1"
+shift
+tmp_dir="/tmp/$(basename "$tar_file")"
+mkdir -p $tmp_dir
+tar -C $tmp_dir -xvf $tar_file
+
+# Run the jar and remove the temporary directory
+java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir"
+rm -rf $tmp_dir
diff -r afa0439120d8 -r 66ad014e6975 samifier/protein_merger.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/protein_merger.xml	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,25 @@
+<tool id="protmerger" name="Protein Merger" version="1.0.9">
+        <description>Virtual Protein Merger</description>
+        <command interpreter="bash">
+        protein_merger.sh virtual_protein_merger.jar $chromosome_tar -g "$genomeFile" -o "$output1" 
+        -r "$searchResultsFile" 
+	#if $trans_tab_file
+	-t "$trans_tab_file"
+	#end if
+	#if $confidence_score
+	-s "$confidence_score"
+	#end if
+        </command>
+        <inputs>
+        	<param name="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" />
+        	<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"/>
+		<param name="confidence_score" type="integer" label="Confidence score thresold" help="Minimum confidence score for peptides to be included" optional="True" />
+	</inputs>
+        <outputs>
+                <data format="sam" name="output1" />
+        </outputs>
+        <help>
+        </help>
+</tool>
diff -r afa0439120d8 -r 66ad014e6975 samifier/result_analyser.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/result_analyser.sh	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# Check java version
+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
+
+# Locate the jar directory
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+jar_path="${DIR}/${1}"
+shift
+
+# Untar the chromosome file into a temporary directory
+tar_file="$1"
+shift
+tmp_dir="/tmp/$(basename "$tar_file")"
+mkdir -p $tmp_dir
+tar -C $tmp_dir -xvf $tar_file
+
+# Run the jar and remove the temporary directory
+java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir"
+rm -rf $tmp_dir
diff -r afa0439120d8 -r 66ad014e6975 samifier/result_analyser.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/result_analyser.xml	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,31 @@
+<tool id="resanalyser" name="Result Analyser" version="1.0.9">
+        <description>Result Analyser</description>
+        <command interpreter="bash">
+        result_analyser.sh results_analyser.jar $chromosome_tar -g "$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="chromosome_tar" type="data" format="tar" label="Select chromosome tar file" help="A Tar file containing all the chromosome files" />
+        	<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 afa0439120d8 -r 66ad014e6975 samifier/results_analyser.jar
Binary file samifier/results_analyser.jar has changed
diff -r afa0439120d8 -r 66ad014e6975 samifier/samifier.jar
Binary file samifier/samifier.jar has changed
diff -r afa0439120d8 -r 66ad014e6975 samifier/samifier.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/samifier.sh	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# Check java version
+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
+
+# Locate the jar directory
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+jar_path="${DIR}/${1}"
+shift
+
+# Untar the chromosome file into a temporary directory
+tar_file="$1"
+shift
+tmp_dir="/tmp/$(basename "$tar_file")"
+mkdir -p $tmp_dir
+tar -C $tmp_dir -xvf $tar_file
+
+# Run the jar and remove the temporary directory
+java -Xmx3072M -jar $jar_path $@ -c "$tmp_dir"
+rm -rf $tmp_dir
diff -r afa0439120d8 -r 66ad014e6975 samifier/samifier.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/samifier.xml	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,46 @@
+<tool id="samifier" name="Samifier" version="1.0.9">
+        <description>Samifier</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 afa0439120d8 -r 66ad014e6975 samifier/tar.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samifier/tar.py	Tue Aug 06 20:43:24 2013 -0400
@@ -0,0 +1,30 @@
+from galaxy.datatypes import data
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.binary import Binary
+from galaxy.datatypes import metadata
+from galaxy.datatypes.sniff import *
+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
+		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" 
\ No newline at end of file
diff -r afa0439120d8 -r 66ad014e6975 samifier/virtual_protein_merger.jar
Binary file samifier/virtual_protein_merger.jar has changed