--- a/split-by-sample.xml	Wed Feb 21 11:54:51 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,84 +0,0 @@
-<tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">
-    <description>create a Flapjack project file from Flapjack formatted input files.</description>
-    <command><![CDATA[
-        python $__tool_directory__/FlapjackProject.py
-        -j $__tool_directory__/lib/flapjack.jar
-        -g $genotypes
-        -s $traits
-        #if $map
-            -m $map
-        #end if
-        #if $name
-            -n $name
-        #end if
-        #if $qtls
-            -q $qtls
-        #end if
-        #if $adv_opts.show_advanced
-            -M "$adv_opts.missingData"
-            -S "$adv_opts.hetSep"
-        #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"/>
-
-        <param format="fjphenotype" name="traits" type="data" label="Flapjack phenotype file"
-            help="Flapjack-formatted (tab-delimited text) input file of phenotype data"/>
-
-        <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="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
-            help="Flapjack-formatted (tab-delimited text) input file of QTL data"
-            optional="true"/>
-
-        <!-- 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="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')"/>
-            </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>
-
-    <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.
-More information on the CreateProject tool can be found here_
-
-.. _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>
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