# HG changeset patch
# User cropgeeks
# Date 1519220874 18000
# Node ID 33eaa535ceb400fdee71adc033fb4fcb07713e3f
# Parent  3ff3493f54d683a62b4e42c2fd92644a70b63e70
Uploaded

diff -r 3ff3493f54d6 -r 33eaa535ceb4 creatematrix.xml
diff -r 3ff3493f54d6 -r 33eaa535ceb4 createproject.xml
diff -r 3ff3493f54d6 -r 33eaa535ceb4 datatypes_conf.xml
diff -r 3ff3493f54d6 -r 33eaa535ceb4 favalleleheadercreator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/favalleleheadercreator.xml	Wed Feb 21 08:47:54 2018 -0500
@@ -0,0 +1,63 @@
+<tool id="intertek_to_flapjack_fav_allele" name="Intertek -> Flapjack favourable allele header formate" version="0.0.1">
+	<description>convert an HDF5 formatted genotype file into a Flapjack formatted genotype file</description>
+	<command><![CDATA[
+		java
+		#if $adv_opts.show_advanced
+			-Xmx$adv_opts.memory
+		#end if
+		-cp $__tool_directory__/lib/intertek-parser.jar jhi.flapjack.io.cmd.IntertekParser
+		-g $genotype
+		-i $intertek
+		-o $output
+	]]></command>
+	<inputs>
+		<param format="txt" name="intertek" type="data" label="Intertek favourable allele file"
+			help="An Intertek file with favourable and unfavourable allele information for markers."/>
+		<param format="fjgenotype" name="genotype" type="data" label="Flapjack genotype file"
+			help="A Flapjack formatted genotype file with markers which match those in the intertek file so that we can
+				add the favourable and unfavourable allele information to this Flapjack genotype file."
+			optional="true"/>
+
+		<conditional name="adv_opts">
+			<param name="show_advanced" type="boolean"
+				   label="Enable advanced options"
+				   truevalue="show" falsevalue="">
+			</param>
+			<when value="show">
+				<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="fjgenotype" 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: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
+	]]></help>
+
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btq580</citation>
+	</citations>
+</tool>
\ No newline at end of file
diff -r 3ff3493f54d6 -r 33eaa535ceb4 fj2hdf5.xml
diff -r 3ff3493f54d6 -r 33eaa535ceb4 flapjack.py
diff -r 3ff3493f54d6 -r 33eaa535ceb4 hapmap2fj.xml
diff -r 3ff3493f54d6 -r 33eaa535ceb4 hdf52fj.xml
diff -r 3ff3493f54d6 -r 33eaa535ceb4 jnlp.xml
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/brapi-client.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/castor-core-1.4.1.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/castor-xml-1.4.1.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/com.fasterxml.jackson.annotations.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/com.fasterxml.jackson.core.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/com.fasterxml.jackson.databind.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/commons-cli-1.4.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/commons-lang3-3.4.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/commons-logging-1.1.1.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/converter-jackson-2.1.0.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/flapjack.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/jcommon-1.0.23.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/jfreechart-1.0.19.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-devel/catalina-ant.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-devel/drmaa.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-devel/junit-4.4.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-devel/servlet-api.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-devel/tomcat-coyote.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-devel/tomcat-juli.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-devel/tomcat-util.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/com.fasterxml.jackson.csv.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/com.fasterxml.jackson.smile.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/com.fasterxml.jackson.xml.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/com.fasterxml.jackson.yaml.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/org.json.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/org.restlet-2.3.1.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/org.restlet.ext.fileupload.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/org.restlet.ext.jackson.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/org.restlet.ext.json.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/org.restlet.ext.servlet.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/lib-servlet/org.restlet.jar
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diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/okhttp-3.4.2.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/okio-1.11.0.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/org.apache.commons.fileupload.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/osxadapter.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/retrofit-2.1.0.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/scri-commons.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/sis-jhdf5-batteries_included.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/sqlite-jdbc-3.7.2.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/xerces-serializer-2.11.0.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/xercesImpl-2.11.0.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 lib/xml-apis.jar
diff -r 3ff3493f54d6 -r 33eaa535ceb4 mabcstats.xml
--- a/mabcstats.xml	Fri Nov 17 06:38:55 2017 -0500
+++ b/mabcstats.xml	Wed Feb 21 08:47:54 2018 -0500
@@ -18,7 +18,7 @@
 		-c $coverage
 		-o $output
 		#if $exclude_parents
-			-e
+			-x
 		#end if
 		#if $adv_opts.show_advanced
 			$adv_opts.allChromosomes
diff -r 3ff3493f54d6 -r 33eaa535ceb4 pedverf1stats.xml
--- a/pedverf1stats.xml	Fri Nov 17 06:38:55 2017 -0500
+++ b/pedverf1stats.xml	Wed Feb 21 08:47:54 2018 -0500
@@ -20,6 +20,9 @@
 		#if $simulate_f1.simulate_f1_selector == False
 			-e $simulate_f1.expectedF1
 		#end if
+		#if $exclude_parents
+			-x
+		#end if
 		#if $adv_opts.show_advanced
 			$adv_opts.allChromosomes
 			$adv_opts.collapseHets
@@ -65,6 +68,10 @@
 			</when>
 		</conditional>
 
+		<param name="exclude_parents" type="boolean" label="Exclude parental lines which have not been selected."
+			   truevalue="true" falsevalue="false" help="Excludes parental lines which have not been selected as the recurrent, or donor parent from the analysis and results.">
+		</param>
+
 		<!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
 		<conditional name="adv_opts">
 			<param name="show_advanced" type="boolean"
diff -r 3ff3493f54d6 -r 33eaa535ceb4 transpose.xml