# HG changeset patch
# User cropgeeks
# Date 1487340990 18000
# Node ID 87dae67fb9a3c1bb8ba309498b10de5e6150f24a
# Parent  7748147a552f4ee0e728b10931a93fec0c66511a
Uploaded

diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/flapjack.xml
--- a/cropgeeks_flapjack/flapjack.xml	Wed Feb 15 06:01:34 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<tool id="jhi_flapjack" 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 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/brapi-client.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/castor-core-1.4.1.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/castor-xml-1.4.1.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/com.fasterxml.jackson.annotations.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/commons-lang3-3.4.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/commons-logging-1.1.1.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/converter-jackson-2.1.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/flapjack.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/jcommon-1.0.23.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/jfreechart-1.0.19.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/okhttp-3.4.2.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/okio-1.11.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/org.apache.commons.fileupload.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/osxadapter.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/retrofit-2.1.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/scri-commons.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/sis-jhdf5-batteries_included.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/sqlite-jdbc-3.7.2.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/xerces-serializer-2.11.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/xercesImpl-2.11.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 cropgeeks_flapjack/lib/xml-apis.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flapjack/datatypes_conf.xml	Fri Feb 17 09:16:30 2017 -0500
@@ -0,0 +1,14 @@
+<?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"/>
+    </registration>
+    <sniffers>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackMapFormat"/>
+       <sniffer type="galaxy.datatypes.flapjack:FlapjackGenotypeFormat"/>
+    </sniffers>
+</datatypes>
diff -r 7748147a552f -r 87dae67fb9a3 flapjack/fj2hdf5.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flapjack/fj2hdf5.xml	Fri Feb 17 09:16:30 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 7748147a552f -r 87dae67fb9a3 flapjack/flapjack.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flapjack/flapjack.py	Fri Feb 17 09:16:30 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 = "jfphenotye"
+
+    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 7748147a552f -r 87dae67fb9a3 flapjack/lib/brapi-client.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/castor-core-1.4.1.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/castor-xml-1.4.1.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/com.fasterxml.jackson.annotations.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/commons-logging-1.1.1.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/converter-jackson-2.1.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/flapjack.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/jcommon-1.0.23.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/jfreechart-1.0.19.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/okhttp-3.4.2.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/okio-1.11.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/org.apache.commons.fileupload.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/osxadapter.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/retrofit-2.1.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/scri-commons.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/sis-jhdf5-batteries_included.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/sqlite-jdbc-3.7.2.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/xerces-serializer-2.11.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/xercesImpl-2.11.0.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/lib/xml-apis.jar
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diff -r 7748147a552f -r 87dae67fb9a3 flapjack/mabcstats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flapjack/mabcstats.xml	Fri Feb 17 09:16:30 2017 -0500
@@ -0,0 +1,92 @@
+<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$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 $decimalEnglish -output=$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="bam" 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"/>
+	<!--<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>-->
+	
+	
+	<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 7748147a552f -r 87dae67fb9a3 flapjack/pedverf1stats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flapjack/pedverf1stats.xml	Fri Feb 17 09:16:30 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