# HG changeset patch
# User cropgeeks
# Date 1487677020 18000
# Node ID 8970bd92145824deb6480bab42444032a1361dd0
# Parent  0d040ceef4792248c6c9288c28316066d32564ad
Uploaded

diff -r 0d040ceef479 -r 8970bd921458 createproject.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/createproject.xml	Tue Feb 21 06:37:00 2017 -0500
@@ -0,0 +1,63 @@
+<tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
+
+<!--System.out.println("Usage: createproject <options>\n"
+				+ " where valid options are:\n"
+				+ "   -map=<map_file>                (optional input file)\n"
+				+ "   -genotypes=<genotypes_file>    (required input file)\n"
+				+ "   -traits=<traits_file>          (optional input file)\n"
+				+ "   -qtls=<qtl_file>               (optional input file)\n"
+				+ "   -decimalEnglish                (optional input parameter)\n"
+				+ "   -project=<project_file>        (required output file)\n");-->
+
+  <description>Run pedigree verification of F1s (known parents) analysis</description>
+  <command><![CDATA[
+  java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject 
+  -map=$map -genotypes=$genotypes -galaxyHTML=$html -project=$output
+  ]]>
+  </command>
+  <inputs>
+    <param format="fjmap" name="map" type="data" label="Flapjack map file"
+		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
+	<param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
+
+	<param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
+            label="Read input data using decimal English"
+            help="Build the index using a perfect hash rather than a dense hash.  This will require less memory
+			(especially during quantification), but will take longer to construct "/>
+	<param name="memory" type="select" label="Memory"
+		help="How much memory to use; larger files may require more memory">
+	  <option selected="true" value="64m">64MB</option>
+	  <option value="128m">128MB</option>
+	  <option value="256m">256MB</option>
+	</param>
+  </inputs>
+  <outputs>
+    <data name="output" format="flapjack" />
+	<data name="html" format="html" />
+  </outputs>
+  
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
+allowing for rapid navigation and comparisons between lines, markers and chromosomes.
+
+This tool creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
+See Flapjack's documentation_ for more details on the various Flapjack data formats.
+
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+
+
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq580</citation>
+  </citations>
+</tool>
\ No newline at end of file
diff -r 0d040ceef479 -r 8970bd921458 datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Tue Feb 21 06:37:00 2017 -0500
@@ -0,0 +1,21 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="flapjack.py"/>
+    </datatype_files>
+    <registration>
+       <datatype extension="flapjack" type="galaxy.datatypes.flapjack:FlapjackProjectFormat" mimetype="application/octet-stream" display_in_upload="true"/>
+	   <datatype extension="fjmap" type="galaxy.datatypes.flapjack:FlapjackMapFormat" mimetype="text/plain" display_in_upload="true"/>
+       <datatype extension="fjgenotype" type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat" mimetype="text/plain" display_in_upload="true"/>
+       <datatype extension="fjphenotype" type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat" mimetype="text/plain" display_in_upload="true"/>
+       <datatype extension="fjqtl" type="galaxy.datatypes.flapjack:FlapjackQtlFormat" mimetype="text/plain" display_in_upload="true"/>
+       <datatype extension="fjgraph" type="galaxy.datatypes.flapjack:FlapjackGraphFormat" mimetype="text/plain" display_in_upload="true"/>
+    </registration>
+    <sniffers>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat"/>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat"/>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackQtlFormat"/>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackGraphFormat"/>
+    </sniffers>
+</datatypes>
diff -r 0d040ceef479 -r 8970bd921458 fj2hdf5.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fj2hdf5.xml	Tue Feb 21 06:37:00 2017 -0500
@@ -0,0 +1,37 @@
+<tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1">
+  <description>convert a Flapjack-formatted genotype file into HDF5</description>
+  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command>
+  <inputs>
+    <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file"
+		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
+	<param name="memory" type="select" label="Memory"
+		help="How much memory to use; larger files may require more memory">
+	  <option selected="true" value="64m">64MB</option>
+	  <option value="128m">128MB</option>
+	  <option value="256m">256MB</option>
+	</param>
+  </inputs>
+  <outputs>
+    <data format="h5" name="output_hdf5" />
+  </outputs>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
+allowing for rapid navigation and comparisons between lines, markers and chromosomes.
+
+This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
+See Flapjack's documentation_ for more details on the various Flapjack data formats.
+
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+
+
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq580</citation>
+  </citations>
+</tool>
\ No newline at end of file
diff -r 0d040ceef479 -r 8970bd921458 flapjack.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flapjack.py	Tue Feb 21 06:37:00 2017 -0500
@@ -0,0 +1,56 @@
+from galaxy.datatypes.data import Text
+
+class FlapjackMapFormat(Text):
+    file_ext = "fjmap"
+
+    def sniff( self, filename ):
+        h = open(filename)
+        line = h.readline()
+        if line.rstrip() != "# fjFile = MAP":
+            h.close()
+            return False
+        return True
+
+class FlapjackGenotypeFormat(Text):
+    file_ext = "fjgenotype"
+
+    def sniff( self, filename ):
+        h = open(filename)
+        line = h.readline()
+        if line.rstrip() != "# fjFile = GENOTYPE":
+            h.close()
+            return False
+        return True
+
+class FlapjackPhenotypeFormat(Text):
+    file_ext = "fjphenotye"
+
+    def sniff( self, filename ):
+        h = open(filename)
+        line = h.readline()
+        if line.rstrip() != "# fjFile = PHENOTYPE":
+            h.close()
+            return False
+        return True
+
+class FlapjackQtlFormat(Text):
+    file_ext = "fjqtl"
+
+    def sniff( self, filename ):
+        h = open(filename)
+        line = h.readline()
+        if line.rstrip() != "# fjFile = QTL":
+            h.close()
+            return False
+        return True
+
+class FlapjackGraphFormat(Text):
+    file_ext = "fjgraph"
+
+    def sniff( self, filename ):
+        h = open(filename)
+        line = h.readline()
+        if line.rstrip() != "# fjFile = GRAPH":
+            h.close()
+            return False
+        return True
\ No newline at end of file
diff -r 0d040ceef479 -r 8970bd921458 flapjack/datatypes_conf.xml
--- a/flapjack/datatypes_conf.xml	Mon Feb 20 08:15:58 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-    <datatype_files>
-        <datatype_file name="flapjack.py"/>
-    </datatype_files>
-    <registration>
-       <datatype extension="fjmap" type="galaxy.datatypes.flapjack:FlapjackMapFormat" mimetype="text/plain" display_in_upload="true"/>
-       <datatype extension="fjgenotype" type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat" mimetype="text/plain" display_in_upload="true"/>
-       <datatype extension="fjphenotype" type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat" mimetype="text/plain" display_in_upload="true"/>
-       <datatype extension="fjqtl" type="galaxy.datatypes.flapjack:FlapjackQtlFormat" mimetype="text/plain" display_in_upload="true"/>
-       <datatype extension="fjgraph" type="galaxy.datatypes.flapjack:FlapjackGraphFormat" mimetype="text/plain" display_in_upload="true"/>
-    </registration>
-    <sniffers>
-       <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/>
-       <sniffer type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat"/>
-       <sniffer type="galaxy.datatypes.flapjack:FlapjackPhenotypeFormat"/>
-       <sniffer type="galaxy.datatypes.flapjack:FlapjackQtlFormat"/>
-       <sniffer type="galaxy.datatypes.flapjack:FlapjackGraphFormat"/>
-    </sniffers>
-</datatypes>
diff -r 0d040ceef479 -r 8970bd921458 flapjack/fj2hdf5.xml
--- a/flapjack/fj2hdf5.xml	Mon Feb 20 08:15:58 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<tool id="flapjack_fj2hdf5" name="Flapjack to HDF5" version="0.0.1">
-  <description>convert a Flapjack-formatted genotype file into HDF5</description>
-  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter -genotypes=$input_genotypes -hdf5=$output_hdf5</command>
-  <inputs>
-    <param format="csv,tabular,txt" name="input_genotypes" type="data" label="Source file"
-		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
-	<param name="memory" type="select" label="Memory"
-		help="How much memory to use; larger files may require more memory">
-	  <option selected="true" value="64m">64MB</option>
-	  <option value="128m">128MB</option>
-	  <option value="256m">256MB</option>
-	</param>
-  </inputs>
-  <outputs>
-    <data format="h5" name="output_hdf5" />
-  </outputs>
-
-  <help><![CDATA[
-.. class:: infomark
-
-**What it does**
-
-Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
-allowing for rapid navigation and comparisons between lines, markers and chromosomes.
-
-This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
-See Flapjack's documentation_ for more details on the various Flapjack data formats.
-
-.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
-
-
-
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
-</tool>
\ No newline at end of file
diff -r 0d040ceef479 -r 8970bd921458 flapjack/flapjack.py
--- a/flapjack/flapjack.py	Mon Feb 20 08:15:58 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-from galaxy.datatypes.data import Text
-
-class FlapjackMapFormat(Text):
-    file_ext = "fjmap"
-
-    def sniff( self, filename ):
-        h = open(filename)
-        line = h.readline()
-        if line.rstrip() != "# fjFile = MAP":
-            h.close()
-            return False
-        return True
-
-class FlapjackGenotypeFormat(Text):
-    file_ext = "fjgenotype"
-
-    def sniff( self, filename ):
-        h = open(filename)
-        line = h.readline()
-        if line.rstrip() != "# fjFile = GENOTYPE":
-            h.close()
-            return False
-        return True
-
-class FlapjackPhenotypeFormat(Text):
-    file_ext = "fjphenotye"
-
-    def sniff( self, filename ):
-        h = open(filename)
-        line = h.readline()
-        if line.rstrip() != "# fjFile = PHENOTYPE":
-            h.close()
-            return False
-        return True
-
-class FlapjackQtlFormat(Text):
-    file_ext = "fjqtl"
-
-    def sniff( self, filename ):
-        h = open(filename)
-        line = h.readline()
-        if line.rstrip() != "# fjFile = QTL":
-            h.close()
-            return False
-        return True
-
-class FlapjackGraphFormat(Text):
-    file_ext = "fjgraph"
-
-    def sniff( self, filename ):
-        h = open(filename)
-        line = h.readline()
-        if line.rstrip() != "# fjFile = GRAPH":
-            h.close()
-            return False
-        return True
\ No newline at end of file
diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/brapi-client.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/castor-core-1.4.1.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/castor-xml-1.4.1.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/com.fasterxml.jackson.annotations.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/com.fasterxml.jackson.core.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/com.fasterxml.jackson.databind.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/commons-lang3-3.4.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/commons-logging-1.1.1.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/converter-jackson-2.1.0.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/flapjack.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/jcommon-1.0.23.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/jfreechart-1.0.19.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/okhttp-3.4.2.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/okio-1.11.0.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/org.apache.commons.fileupload.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/osxadapter.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/retrofit-2.1.0.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/scri-commons.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/sis-jhdf5-batteries_included.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/sqlite-jdbc-3.7.2.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/xerces-serializer-2.11.0.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/xercesImpl-2.11.0.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/lib/xml-apis.jar
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diff -r 0d040ceef479 -r 8970bd921458 flapjack/mabcstats.xml
--- a/flapjack/mabcstats.xml	Mon Feb 20 08:15:58 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
-
-<!--System.out.println("Usage: mabcstats <options>\n"
-				+ " where valid options are:\n"
-				+ "   -map=<map_file>                (required input file)\n"
-				+ "   -genotypes=<genotypes_file>    (required input file)\n"
-				+ "   -qtls=<qtl_file>               (required input file)\n"
-				+ "   -parent1=<index_of_line>       (required parameter, first line is index 1)\n"
-				+ "   -parent2=<index_of_line>       (required parameter, first line is index 1)\n"
-				+ "   -model=weighted|unweighted     (required parameter)\n"
-				+ "   -coverage=<coverage_value>     (optional floating point parameter)\n"
-				+ "   -decimalEnglish                (optional parameter)\n"
-				+ "   -output=<output_file>          (required output file)");-->
-
-  <description>Run marker assisted backcrossing analysis on a dataset</description>
-  <command>java -Xmx$advanced_options.memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats -map=$map -genotypes=$genotypes -qtls=$qtls -parent1=$parent1 -parent2=$parent2 -model=$model -coverage=$coverage $advanced_options.decimalEnglish -output=$output</command>
-  <inputs>
-    <param format="fjmap" name="map" type="data" label="Flapjack map file"
-		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
-	<param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
-		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
-	<param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
-		help="Flapjack-formatted (tab-delimited text) input file of QTL data"/>
-	<param name="parent1" type="integer" value="1" label="Index of recurrent parent"
-		help="The index of the recurrent parent in the genotype file"/>
-	<param name="parent2" type="integer" value="2" label="Index of donor parent"
-		help="The index of the donor parent in the genotype file"/>
-	<param name="model" type="select" label="Model"
-		help="The model to use for calculating statistics">
-	  <option selected="true" value="weighted">Weighted</option>
-	  <option value="unweighted">Unweighted</option>
-	</param>
-	<param name="coverage" type="integer" value="10" label="Maximum coverage of a marker"
-		help="The maximum length of genome a marker can represent"/>
-	
-	<conditional name="advanced_options">
-		<param name="show_advanced" type="boolean" label="Show advanced options"
-			truevalue="show" falsevalue="">
-		</param>
-		<when value="show">
-			<param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
-            label="Use English-style decimal marks"
-            help="Process input data using '.' as the decimal separator (as opposed to ',')"/>
-			<param name="memory" type="select" label="Memory"
-				help="How much memory to use; larger files may require more memory">
-			  <option selected="true" value="64m">64MB</option>
-			  <option value="128m">128MB</option>
-			  <option value="256m">256MB</option>
-			</param>
-		</when>
-	</conditional>
-	
-	
-  </inputs>
-  <outputs>
-    <data format="tabular" name="output" />
-  </outputs>
-  
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-
-  <help><![CDATA[
-.. class:: infomark
-
-**What it does**
-
-Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
-allowing for rapid navigation and comparisons between lines, markers and chromosomes.
-
-This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
-See Flapjack's documentation_ for more details on the various Flapjack data formats.
-
-.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
-
-
-
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
-</tool>
\ No newline at end of file
diff -r 0d040ceef479 -r 8970bd921458 flapjack/pedverf1stats.xml
--- a/flapjack/pedverf1stats.xml	Mon Feb 20 08:15:58 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-<tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">
-
-<!--System.out.println("Usage: pedverf1sstats <options>\n"
-				+ " where valid options are:\n"
-				+ "   -map=<map_file>                (required input file)\n"
-				+ "   -genotypes=<genotypes_file>    (required input file)\n"
-				+ "   -parent1=<index_of_line>       (required parameter, first line is index 1)\n"
-				+ "   -parent2=<index_of_line>       (required parameter, first line is index 1)\n"
-				+ "   -expectedf1=<index_of_line>    (optional parameter, first line is index 1)\n"
-				+ "   -decimalEnglish                (optional parameter)\n"
-				+ "   -output=<output_file>          (required output file)\n");-->
-
-  <description>Run pedigree verification of F1s (known parents) analysis</description>
-  <command><![CDATA[
-  java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats 
-  -map=$map -genotypes=$genotypes -parent1=$parent1 -parent2=$parent2 
-  #if $simulate_f1.simulate_f1_selector == "file":
-	-expectedf1=$simulate_f1.expectedF1
-  #end if
-  $decimalEnglish -output=$output
-  ]]>
-  </command>
-  <inputs>
-    <param format="csv,tabular,txt" name="map" type="data" label="Flapjack map file"
-		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
-	<param format="csv,tabular,txt" name="genotypes" type="data" label="Flapjack genotype file"
-		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
-	<param name="parent1" type="integer" value="1" label="Index of parent 1"
-		help="The index of the first parent in the genotype file"/>
-	<param name="parent2" type="integer" value="2" label="Index of parent 2"
-		help="The index of the second parent in the genotype file"/>
-		
-	<conditional name="simulate_f1">
-		<param name="simulate_f1_selector" type="select" label="Simulate expected F1 (or use F1 from file)">
-			<option value="simulate" selected="True">Simulate</option>
-			<option value="file">Select from file</option>
-		</param>
-		<when value="file">
-			<param argument="-expectedF1" type="integer" value="3" label="Index of expected F1"
-			help="The index of the donor parent in the genotype file"/>
-		</when>
-	</conditional>
-
-	<param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
-            label="Read input data using decimal English"
-            help="Build the index using a perfect hash rather than a dense hash.  This will require less memory
-			(especially during quantification), but will take longer to construct "/>
-	<param name="memory" type="select" label="Memory"
-		help="How much memory to use; larger files may require more memory">
-	  <option selected="true" value="64m">64MB</option>
-	  <option value="128m">128MB</option>
-	  <option value="256m">256MB</option>
-	</param>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="output" />
-  </outputs>
-  
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-
-  <help><![CDATA[
-.. class:: infomark
-
-**What it does**
-
-Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
-allowing for rapid navigation and comparisons between lines, markers and chromosomes.
-
-This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
-See Flapjack's documentation_ for more details on the various Flapjack data formats.
-
-.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
-
-
-
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
-</tool>
\ No newline at end of file
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diff -r 0d040ceef479 -r 8970bd921458 mabcstats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mabcstats.xml	Tue Feb 21 06:37:00 2017 -0500
@@ -0,0 +1,85 @@
+<tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
+
+  <description>Run marker assisted backcrossing analysis on a dataset</description>
+
+  <command><![CDATA[
+  java
+  #if $advanced_options.show_advanced
+    -Xmx$advanced_options.memory
+  #end if
+  -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
+  -map=$map
+  -genotypes=$genotypes
+  -qtls=$qtls
+  -parent1=$parent1
+  -parent2=$parent2
+  -model=$model
+  -coverage=$coverage
+  #if $advanced_options.show_advanced
+    $advanced_options.decimalEnglish
+  #end if
+  -output=$output
+  ]]></command>
+
+  <inputs>
+    <param format="fjmap" name="map" type="data" label="Flapjack map file"
+		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
+	<param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
+	<param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
+		help="Flapjack-formatted (tab-delimited text) input file of QTL data"/>
+	<param name="parent1" type="integer" value="1" label="Index of recurrent parent"
+		help="The index of the recurrent parent in the genotype file"/>
+	<param name="parent2" type="integer" value="2" label="Index of donor parent"
+		help="The index of the donor parent in the genotype file"/>
+	<param name="model" type="select" label="Model"
+		help="The model to use for calculating statistics">
+	  <option selected="true" value="weighted">Weighted</option>
+	  <option value="unweighted">Unweighted</option>
+	</param>
+	<param name="coverage" type="float" value="10" label="Maximum coverage of a marker"
+		help="The maximum length of genome a marker can represent"/>
+	<conditional name="advanced_options">
+		<param name="show_advanced" type="boolean" label="Enable advanced options"
+			truevalue="show" falsevalue="">
+		</param>
+		<when value="show">
+			<param name="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
+            label="Force English-style decimal marks"
+            help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/>
+			<param name="memory" type="select" label="Memory"
+				help="How much memory to use; larger files may require more memory">
+			  <option selected="true" value="64m">64MB</option>
+			  <option value="128m">128MB</option>
+			  <option value="256m">256MB</option>
+			</param>
+		</when>
+	</conditional>	
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+  
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
+allowing for rapid navigation and comparisons between lines, markers and chromosomes.
+
+This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
+See Flapjack's documentation_ for more details on the various Flapjack data formats.
+
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq580</citation>
+  </citations>
+</tool>
\ No newline at end of file
diff -r 0d040ceef479 -r 8970bd921458 pedverf1stats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pedverf1stats.xml	Tue Feb 21 06:37:00 2017 -0500
@@ -0,0 +1,82 @@
+<tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">
+
+<!--System.out.println("Usage: pedverf1sstats <options>\n"
+				+ " where valid options are:\n"
+				+ "   -map=<map_file>                (required input file)\n"
+				+ "   -genotypes=<genotypes_file>    (required input file)\n"
+				+ "   -parent1=<index_of_line>       (required parameter, first line is index 1)\n"
+				+ "   -parent2=<index_of_line>       (required parameter, first line is index 1)\n"
+				+ "   -expectedf1=<index_of_line>    (optional parameter, first line is index 1)\n"
+				+ "   -decimalEnglish                (optional parameter)\n"
+				+ "   -output=<output_file>          (required output file)\n");-->
+
+  <description>Run pedigree verification of F1s (known parents) analysis</description>
+  <command><![CDATA[
+  java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats 
+  -map=$map -genotypes=$genotypes -parent1=$parent1 -parent2=$parent2 
+  #if $simulate_f1.simulate_f1_selector == "file":
+	-expectedf1=$simulate_f1.expectedF1
+  #end if
+  $decimalEnglish -output=$output
+  ]]>
+  </command>
+  <inputs>
+    <param format="csv,tabular,txt" name="map" type="data" label="Flapjack map file"
+		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
+	<param format="csv,tabular,txt" name="genotypes" type="data" label="Flapjack genotype file"
+		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
+	<param name="parent1" type="integer" value="1" label="Index of parent 1"
+		help="The index of the first parent in the genotype file"/>
+	<param name="parent2" type="integer" value="2" label="Index of parent 2"
+		help="The index of the second parent in the genotype file"/>
+		
+	<conditional name="simulate_f1">
+		<param name="simulate_f1_selector" type="select" label="Simulate expected F1 (or use F1 from file)">
+			<option value="simulate" selected="True">Simulate</option>
+			<option value="file">Select from file</option>
+		</param>
+		<when value="file">
+			<param argument="-expectedF1" type="integer" value="3" label="Index of expected F1"
+			help="The index of the donor parent in the genotype file"/>
+		</when>
+	</conditional>
+
+	<param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
+            label="Read input data using decimal English"
+            help="Build the index using a perfect hash rather than a dense hash.  This will require less memory
+			(especially during quantification), but will take longer to construct "/>
+	<param name="memory" type="select" label="Memory"
+		help="How much memory to use; larger files may require more memory">
+	  <option selected="true" value="64m">64MB</option>
+	  <option value="128m">128MB</option>
+	  <option value="256m">256MB</option>
+	</param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+  
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+
+  <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
+allowing for rapid navigation and comparisons between lines, markers and chromosomes.
+
+This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
+See Flapjack's documentation_ for more details on the various Flapjack data formats.
+
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+
+
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btq580</citation>
+  </citations>
+</tool>
\ No newline at end of file