# HG changeset patch
# User cropgeeks
# Date 1510659768 18000
# Node ID 8855844f40a8e43bd114b14ec9f9218f881788a6
# Parent  1de63acd6b12db61bdd3502d0edd323592e3a061
Uploaded the latest version of our Flapjack tools for Galaxy.

diff -r 1de63acd6b12 -r 8855844f40a8 creatematrix.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/creatematrix.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -0,0 +1,107 @@
+<tool id="flapjack_creatematrix" name="Flapjack Create Similarity Matrix" version="0.0.1">
+    <description>Create a similarity matrix from the given Genotype file</description>
+    <command><![CDATA[
+        java
+        #if $adv_opts.show_advanced
+            -Xmx$adv_opts.memory
+        #end if
+        -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateMatrix
+        -g $genotypes
+        -o $output
+        #if $map
+            -m $map
+        #end if
+        #if $adv_opts.show_advanced
+            $adv_opts.allChromosomes
+            $adv_opts.collapseHets
+            -M "$adv_opts.missingData"
+            -S "$adv_opts.hetSep"
+            $adv_opts.transposed
+            $adv_opts.decimalEnglish
+        #end if
+        #if $create_project
+            -p $project
+        #end if
+    ]]></command>
+    <inputs>
+        <param format="fjmap" name="map" type="data" label="Flapjack map file"
+            help="Flapjack-formatted (tab-delimited text) input file of map data"
+            optional="true"/>
+        <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
+
+        <!-- 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"
+                label="Enable advanced options"
+                truevalue="show" falsevalue="">
+            </param>
+            <when value="show">
+                <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
+                    label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
+                    help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
+
+                <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
+                    label="Don't distinguish between heterozygous alleles"
+                    help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
+
+                <param name="missingData" type="text" value="-"
+                    label="Missing data string"
+                    help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
+
+                <param name="hetSep" type="text" value="/"
+                    label="Heterozygous allele separator string"
+                    help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
+
+                <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
+                    label="Genotype data has been transposed"
+                    help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
+
+                <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
+                    label="Force English-style decimal marks"
+                    help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server'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>
+        <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
+
+        <param name="create_project" type="boolean" label="Also create Flapjack project file"
+            truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the generated similarity matrix.">
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="output" />
+        <data format="flapjack" name="project">
+            <filter>create_project</filter>
+        </data>
+    </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.
+
+Flapjack documentation_
+
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#creatematrix-exe-jhi-flapjack-io-creatematrix
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq580</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 1de63acd6b12 -r 8855844f40a8 createproject.xml
--- a/createproject.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/createproject.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,50 +1,107 @@
 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
+    <description>Create a Flapjack project file from the given input files.</description>
+    <command><![CDATA[
+        java
+        #if $adv_opts.show_advanced
+            -Xmx$adv_opts.memory
+        #end if
+        -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject
+        -g $genotypes
+        -p $output
+        #if $map
+            -m $map
+        #end if
+        #if $name
+            -n $name
+        #end if
+        #if $qtls
+            -q $qtls
+        #end if
+        #if $traits
+            -t $traits
+        #end if
+        #if $adv_opts.show_advanced
+            $adv_opts.allChromosomes
+            $adv_opts.collapseHets
+            -M "$adv_opts.missingData"
+            -S "$adv_opts.hetSep"
+            $adv_opts.transposed
+            $adv_opts.decimalEnglish
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
 
-<!--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");-->
+        <param format="fjmap" name="map" type="data" label="Flapjack map file"
+            help="Flapjack-formatted (tab-delimited text) input file of map data"
+            optional="true"/>
+
+        <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file"
+            help="Flapjack-formatted (tab-delimited text) input file of phenotype data"
+            optional="true"/>
+
+        <param format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
+            help="Flapjack-formatted (tab-delimited text) input file of QTL data"
+            optional="true"/>
+
+        <param format="text" name="name" type="text" label="Optional dataset name"
+            help="The name for the dataset within Flapjack"
+            optional="true"/>
 
-  <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"/>
+        <!-- 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"
+               label="Enable advanced options"
+               truevalue="show" falsevalue="">
+            </param>
+            <when value="show">
+                <param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
+                    label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
+                    help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
+
+                <param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
+                    label="Don't distinguish between heterozygous alleles"
+                    help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
+
+                <param name="missingData" type="text" value="-"
+                    label="Missing data string"
+                    help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
+
+                <param name="hetSep" type="text" value="/"
+                    label="Heterozygous allele separator string"
+                    help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
 
-	<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>
-  <!-- label="${tool.name} on ${on_string}: project.flapjack" -->
-    <data name="output" format="flapjack" />
-	<!--<data name="html" format="html" />-->
-  </outputs>
+                <param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
+                    label="Genotype data has been transposed"
+                    help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
+
+                <param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
+                    label="Force English-style decimal marks"
+                    help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server'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>
+        <!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
+    </inputs>
+
+    <outputs>
+        <data name="output" format="flapjack" />
+    </outputs>
   
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
 
-  <help><![CDATA[
+    <help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -54,13 +111,13 @@
 
 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 
-
-
+More information on the CreateProject tool can be found here_
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
+.. _here: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#createproject-exe-jhi-flapjack-io-createproject
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq580</citation>
+    </citations>
 </tool>
\ No newline at end of file
diff -r 1de63acd6b12 -r 8855844f40a8 datatypes_conf.xml
--- a/datatypes_conf.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/datatypes_conf.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -4,21 +4,21 @@
         <datatype_file name="flapjack.py"/>
     </datatype_files>
     <registration>
-       <datatype extension="flapjack" type="galaxy.datatypes.flapjack:FlapjackFormat" display_in_upload="true">
-	     <display file="jnlp.xml"/>
-	   </datatype>
-	   <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"/>
+        <datatype extension="flapjack" type="galaxy.datatypes.flapjack:FlapjackFormat" display_in_upload="true">
+            <display file="jnlp.xml"/>
+        </datatype>
+        <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:FlapjackFormat"/>
-	   <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"/>
+        <sniffer type="galaxy.datatypes.flapjack:FlapjackFormat"/>
+        <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 1de63acd6b12 -r 8855844f40a8 fj2hdf5.xml
--- a/fj2hdf5.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/fj2hdf5.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,21 +1,44 @@
 <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>
+    <description>Convert a Flapjack-formatted genotype file into HDF5</description>
+    <command><![CDATA[
+        java
+        #if $adv_opts.show_advanced
+            -Xmx$adv_opts.memory
+        #end if
+        -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.FJTabbedToHdf5Converter
+        -g $genotypes
+        -h $output
+    ]]></command>
+    <inputs>
+        <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
+            help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
 
-  <help><![CDATA[
+        <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="h5" name="output" />
+    </outputs>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -26,12 +49,10 @@
 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 
-
-
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
+    ]]></help>
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq580</citation>
+    </citations>
 </tool>
\ No newline at end of file
diff -r 1de63acd6b12 -r 8855844f40a8 flapjack.py
diff -r 1de63acd6b12 -r 8855844f40a8 hapmap2fj.xml
--- a/hapmap2fj.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/hapmap2fj.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,42 +1,51 @@
 <tool id="flapjack_hapmap2fj" name="HapMap to Flapjack" version="0.0.1">
+    <description>Convert a HapMap-formatted 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/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter
+        -h $hapmap
+        -s $separator
+        -m $map
+        -g $genotypes
+    ]]></command>
+    <inputs>
+        <param format="txt" name="hapmap" type="data" label="Source file"
+            help="HapMap Formatted File"/>
 
-<!--System.out.println("Usage: hapmap2flapjack <options>\n"
-			+ " where valid options are:\n"
-			+ "   -separator=<s or t>            (required separator used in input file)\n"
-			+ "   -hapmap=<hapmap_file>          (required input file)\n"
-			+ "   -map=<map_file>                (required output file)\n"
-			+ "   -genotypes=<genotype_file>     (required output file)\n");-->
+        <param name="separator" type="boolean" label="File is tab-separated"
+            truevalue="t" falsevalue="s">
+        </param>
 
-  <description>convert an HapMap formatted file into a Flapjack-formatted genotype file</description>
-  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.HapMapToFJTabbedConverter 
-	  -hapmap=$hapmap
-	  -separator=$separator 
-	  -map=$map
-	  -genotypes=$genotypes
-  </command>
-  <inputs>
-    <param format="txt" name="hapmap" type="data" label="Source file"
-		help="HapMap Formatted File"/>
-	<param name="separator" type="boolean" label="File is tab-separated"
-		truevalue="t" falsevalue="s">
-	</param>
-	<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="fjmap" name="map" />
-    <data format="fjgenotype" name="genotypes" />
-  </outputs>
-  
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+        <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>
 
-  <help><![CDATA[
+    <outputs>
+        <data format="fjmap" name="map" />
+        <data format="fjgenotype" name="genotypes" />
+    </outputs>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -47,12 +56,10 @@
 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 
-
-
+.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats
+    ]]></help>
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btq580</citation>
+    </citations>
 </tool>
\ No newline at end of file
diff -r 1de63acd6b12 -r 8855844f40a8 hdf52fj.xml
--- a/hdf52fj.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/hdf52fj.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,39 +1,56 @@
 <tool id="flapjack_hdf52fj" name="HDF5 to Flapjack" 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/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter
+		-h $hdf5
+		-o $genotypes
+		#if $lines
+			-l $lines
+		#end if
+		#if $markers
+			-m $markers
+		#end if
+	]]></command>
+	<inputs>
+		<param format="h5" name="hdf5" type="data" label="A Flapjack HDF5 genotype file"
+			help="Flapjack's flavour of HDF5 for storing genotype data."/>
+		<param format="txt" name="lines" type="data" label="Line file"
+			help="A list of lines desired in the output. One line name per line on each line of the file."
+			optional="true"/>
+		<param format="txt" name="markers" type="data" label="Marker file"
+			help="A list of markers desired in the output. One line name per marker on each line of the file."
+			optional="true"/>
 
-  <description>convert an HDF5 formatted genotype file into a Flapjack-formatted genotype file</description>
-  <command>java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Hdf5ToFJTabbedConverter 
-	  -hdf5=$hdf5 
-	  -lines=$lines
-	  -markers=$markers
-	  -missing_filter=$missing_filter
-	  -heterozygous_filter=$heterozygous_filter
-	  -genotypes=$genotypes
-  </command>
-  <inputs>
-    <param format="h5" name="hdf5" type="data" label="Source file"
-		help="Flapjack's flavour of HDF5 for storing genotype data."/>
-	<param format="txt" name="lines" type="data" label="Source file"
-		help="A list of lines desired in the output. One line name per line on each line of the file."/>
-	<param format="txt" name="markers" type="data" label="Source file"
-		help="A list of markers desired in the output. One line name per marker on each line of the file."/>
-	<param name="missing_filter" type="boolean" label="Filter out missing markers"
-		truevalue="true" falsevalue="false">
-	</param>
-	<param name="heterozygous_filter" type="boolean" label="Filter out heterozygous markers"
-		truevalue="true" falsevalue="false">
-	</param>
-	<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="fjgenotype" name="genotypes" />
-  </outputs>
+		<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>
 
-  <help><![CDATA[
+	<outputs>
+		<data format="fjgenotype" name="genotypes" />
+	</outputs>
+
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
+
+	<help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -44,12 +61,10 @@
 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 
-
-
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
+	]]></help>
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btq580</citation>
+	</citations>
 </tool>
\ No newline at end of file
diff -r 1de63acd6b12 -r 8855844f40a8 lib/brapi-client.jar
Binary file lib/brapi-client.jar has changed
diff -r 1de63acd6b12 -r 8855844f40a8 lib/flapjack.jar
Binary file lib/flapjack.jar has changed
diff -r 1de63acd6b12 -r 8855844f40a8 lib/scri-commons.jar
Binary file lib/scri-commons.jar has changed
diff -r 1de63acd6b12 -r 8855844f40a8 mabcstats.xml
--- a/mabcstats.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/mabcstats.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,82 +1,120 @@
 <tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">
-
-  <description>Run marker assisted backcrossing analysis on a dataset</description>
+	<description>Run marker assisted backcrossing (MABC) analysis on a dataset</description>
+	<command><![CDATA[
+		java
+		#if $adv_opts.show_advanced
+			-Xmx$adv_opts.memory
+		#end if
+		-cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
+		-m $map
+		-g $genotypes
+		-q $qtls
+		-r $parent1
+		-d $parent2
+		-model $model
+		-c $coverage
+		-o $output
+		#if $adv_opts.show_advanced
+			$adv_opts.allChromosomes
+			$adv_opts.collapseHets
+			-M "$adv_opts.missingData"
+			-S "$adv_opts.hetSep"
+			$adv_opts.transposed
+			$adv_opts.decimalEnglish
+		#end if
+		#if $create_project
+			-p $project
+		#end if
+	]]></command>
 
-  <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
-  -m $map
-  -g $genotypes
-  -q $qtls
-  -r $parent1
-  -d $parent2
-  -model $model
-  -c $coverage
-  #if $advanced_options.show_advanced
-    $advanced_options.decimalEnglish
-  #end if
-  -o $output
-  #if $create_project  
-    -p $project
-  #end if	
-  ]]></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>
 
-  <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 name="coverage" type="float" value="10" label="Maximum coverage of a marker"
+			help="The maximum length of genome a marker can represent."/>
+
+		<conditional name="adv_opts">
+			<param name="show_advanced" type="boolean"
+				label="Enable advanced options"
+				truevalue="show" falsevalue="">
+			</param>
+			<when value="show">
+				<param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
+					label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
+					help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
+
+				<param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
+					label="Don't distinguish between heterozygous alleles"
+					help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
+
+				<param name="missingData" type="text" value="-"
+					label="Missing data string"
+					help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
+
+				<param name="hetSep" type="text" value="/"
+					label="Heterozygous allele separator string"
+					help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
+
+				<param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
+					label="Genotype data has been transposed"
+					help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
+
+				<param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
+					label="Force English-style decimal marks"
+					help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server'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>
+
+		<param name="create_project" type="boolean" label="Also create Flapjack project file"
+			truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
 		</param>
-		<when value="show">
-			<param name="decimalEnglish" type="boolean" truevalue="-D" 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>
-	
-	<param name="create_project" type="boolean" label="Also create Flapjack project file"
-		truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
-	</param>
-  </inputs>
+	</inputs>
   
-  <outputs>
-    <data format="tabular" name="output" />
-	<data format="flapjack" name="project">
-		<filter>create_project</filter>
-	</data> 
-	
-  </outputs>
+	<outputs>
+		<data format="tabular" name="output" />
+		<data format="flapjack" name="project">
+			<filter>create_project</filter>
+		</data>
+	</outputs>
   
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
 
-  <help><![CDATA[
+	<help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -84,13 +122,12 @@
 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.
+Flapjack documentation_
 
-.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#mabcstats-exe-jhi-flapjack-io-generatemabcstats
+	]]></help>
 
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btq580</citation>
+	</citations>
 </tool>
\ No newline at end of file
diff -r 1de63acd6b12 -r 8855844f40a8 pedverf1stats.xml
--- a/pedverf1stats.xml	Tue Aug 29 08:15:12 2017 -0400
+++ b/pedverf1stats.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -1,66 +1,112 @@
 <tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">
+	<description>Run pedigree verification of F1s (known parents) analysis</description>
+	<command><![CDATA[
+		java
+		#if $adv_opts.show_advanced
+			-Xmx$adv_opts.memory
+		#end if
+		-cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats
+		-m $map
+		-g $genotypes
+		-f $parent1
+		-s $parent2
+		-o $output
+		#if $simulate_f1.simulate_f1_selector == False
+			-e $simulate_f1.expectedF1
+		#end if
+		#if $adv_opts.show_advanced
+			$adv_opts.allChromosomes
+			$adv_opts.collapseHets
+			-M "$adv_opts.missingData"
+			-S "$adv_opts.hetSep"
+			$adv_opts.transposed
+			$adv_opts.decimalEnglish
+		#end if
+		#if $create_project
+			-p $project
+		#end if
+	]]></command>
+	<inputs>
+		<param format="fjmap" name="map" type="data" label="Flapjack map file"
+			help="Flapjack-formatted (tab-delimited text) input file of map data"/>
 
-<!--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");-->
+		<param format="fjgenotype" 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="boolean" label="Simulate expected F1 (or use F1 from file)"
+				truevalue="" falsevalue="show" checked="true">
+			</param>
+			<when value="show">
+				<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>
 
-  <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="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 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>
+		<!-- 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"
+				 label="Enable advanced options"
+				 truevalue="show" falsevalue="">
+			</param>
+			<when value="show">
+				<param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
+					label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
+					help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>
+
+				<param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
+					label="Don't distinguish between heterozygous alleles"
+					help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>
+
+				<param name="missingData" type="text" value="-"
+					label="Missing data string"
+					help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>
+
+				<param name="hetSep" type="text" value="/"
+					label="Heterozygous allele separator string"
+					help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>
+
+				<param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
+					label="Genotype data has been transposed"
+					help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>
+
+				<param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
+					label="Force English-style decimal marks"
+					help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server'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>
+		<!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
+		<param name="create_project" type="boolean" label="Also create Flapjack project file"
+			truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the pedigree verification of F1s (known parents) results.">
 		</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>
+	</inputs>
 
-	<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>
+	<outputs>
+		<data format="tabular" name="output" />
+		<data format="flapjack" name="project">
+			<filter>create_project</filter>
+		</data>
+	</outputs>
   
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
 
-  <help><![CDATA[
+	<help><![CDATA[
 .. class:: infomark
 
 **What it does**
@@ -68,15 +114,12 @@
 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.
+Flapjack documentation_
 
-.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 
-
+.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#pedverf1stats-exe-jhi-flapjack-io-generatepedverf1sstats
+	]]></help>
 
-
-  ]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/btq580</citation>
-  </citations>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btq580</citation>
+	</citations>
 </tool>
\ No newline at end of file
diff -r 1de63acd6b12 -r 8855844f40a8 transpose.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/transpose.xml	Tue Nov 14 06:42:48 2017 -0500
@@ -0,0 +1,27 @@
+<tool id="flapjack_transpose" name="Transpose" version="0.0.1">
+	<description>Transpose a file's contents</description>
+	<command><![CDATA[
+		java 
+		-cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.Transpose 
+		$input 
+		$output
+		]]></command>
+	<inputs>
+		<param format="tabular" name="input" type="data" label="Source file"/>
+	</inputs>
+	<outputs>
+		<data format="tabular" name="output" />
+	</outputs>
+
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
+
+	<help><![CDATA[
+.. class:: infomark
+
+**What it does**
+This tool transposes data files.
+	]]></help>
+
+</tool>
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