--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/my_VDM_tool.xml	Fri Nov 06 16:38:33 2020 +0000
@@ -0,0 +1,198 @@
+ <tool id="my_VDM_tool" name="VDM_tool" version="1.0.0">
+<!--A simple description of the tool that will appear in the tool panel in Galaxy.-->
+<description>Map a mutation using in silico bulk segregant linkage analysis of pooled recombinant lines generated through backcrossing.</description>
+<!-- Handles exit codes in Galaxy. -->
+<stdio>
+	<exit_code range="1:"/>
+</stdio>
+<requirements>
+	<requirement type="package" version="3.2.1">R</requirement>
+	<requirement type="package" version="1.2.0">getopt</requirement>
+</requirements>
+
+<command>
+Rscript /home/fxue/galaxy/tools/my_VDM_tool/my_VDM_tool.R
+	--inf "$inf"
+	#if $species.species_select=="Celegans"
+		--itype "$species.ce"
+	#else if $species.species_select=="Zebrafish"
+		--itype "$species.ze"
+	#else if $species.species_select=="Brachypodium"
+		--itype "$species.br"
+	#else if $species.species_select=="Arabidopsis"
+		--itype "$species.ar"
+	#else if $species.species_select=="other"
+		--itype "$species.ot"
+	#end if
+		
+	--qual $qual 
+	--thrup $thrup 
+	--thrlow $thrlow
+	
+	#if $allfreq.allfreq_select=="AB"
+		--allr "$allfreq.ab"
+	#else if $allfreq.allfreq_select=="ratio"
+		--allr "$allfreq.ratio"
+	#end if
+	
+	#if $only_snp.only_snp_select=="TRUE"
+		--snp "$only_snp.true"
+	#else if $only_snp.only_snp_select=="FALSE"
+		--snp "$only_snp.false"
+	#end if
+	
+	--lsp $lsp 
+	--pcol "$pcol" 
+	--lcol "$lcol" 
+	
+	#if $xaxis.xaxis_select=="TRUE"
+		--xstand $xaxis.true
+	#else if $xaxis.xaxis_select=="FALSE"
+		--xstand $xaxis.false
+	#end if
+	
+	--bsize $bsize
+
+	#if $binnorm.binnorm_select=="TRUE"
+		--bnorm $binnorm.true
+	#else if $binnorm.binnorm_select=="FALSE"
+		--bnorm $binnorm.false
+	#end if
+
+	#if $exclfiles.exclfiles_select=="FALSE"
+		--exclf $exclfiles.false
+	#else if $exclfiles.exclfiles_select=="TRUE"
+		--exclf $exclfiles.true
+	#end if
+	
+	
+	--exclthr $exclthr
+	--exclcol "$exclcol" 
+
+	--parn "$parn"
+	--outn "$outn"
+	--pdfn "$pdfn"
+	
+</command>
+<inputs>
+<param type="data" name="inf" format="vcf" label="fastq file"/>
+
+<conditional name="species">
+	<param name="species_select" type="select" label="Select the species">
+		<option value="Celegans">C. elegans</option>
+		<option value="Zebrafish">Zebrafish</option>
+		<option value="Brachypodium">Brachypodium</option>
+		<option value="Arabidopsis">Arabidopsis</option>
+		<option value="other">other</option>
+	</param>
+	<when value="Celegans">
+		<param name="ce" type="hidden" value="C.elegans" label="The C. elegans chromosome numbers and lengths (in Mb)" help="C.elegans help"/>
+	</when>
+	<when value="Zebrafish">
+		<param name="ze" type="hidden" value="Zebrafish" label="The Zebrafish chromosome numbers and lengths (in Mb)" help="Zebrafish help"/>
+	</when>
+	<when value="Brachypodium">
+		<param name="br" type="hidden" value="Brachypodium" label="The Brachypodium chromosome numbers and lengths (in Mb)" help="Brachypodium help"/>
+	</when>
+	<when value="Arabidopsis">
+		<param name="ar" type="hidden" value="Arabidopsis" label="The Arabidopsis chromosome numbers and lengths (in Mb)" help="Arabidopsis help"/>
+	</when>
+	<when value="other">
+		<param name="ot" type="data" format="tabular" label="Select file with chromosome numbers and lengths (in Mb) from your history" help="Table consisting of chromosome number in column 1 and length (in Mb) in column 2 (e.g. 'CHRI	16' or 'CHR1	16') with no column header names, tab-delimitation, and no quotation marks in a .txt file"/>
+	</when>
+</conditional>
+	
+<param type="float" name="qual" value="200" label="Filter by quality" help="Filter results based on quality value"/>
+<param type="float" name="thrup" value="1" label="upper threshold for homozygosity" help="Allele frequency values greater than or equal to this will be considered as homozygous ALT for barplots of frequency homozygous variants along chromosomes"/>
+<param type="float" name="thrlow" value="0" label="lower threshold for homozygosity" help="Allele frequency values less than or equal to this will be considered as homozygous for barplots of frequency homozygous REF variants along chromosomes"/>
+
+
+<conditional name="allfreq">
+	<param name="allfreq_select" type="select" label="Select the source for allele frequency">
+		<option value="AB">AB</option>
+		<option value="ratio">AO/(AO+RO)</option>
+	</param>
+	<when value="AB">
+		<param name="ab" type="hidden" value="AB" label="Use AB field (from Freebayes) as the value for allele frequency" help=" "/>
+	</when>
+	<when value="ratio">
+		<param name="ratio" type="hidden" value="ratio" label="Use AO/(AO+RO) calculation (from Freebayes) as the value for allele frequency" help=" "/>
+	</when>
+	</conditional>
+
+<conditional name="only_snp">
+	<param name="only_snp_select" type="select" label="Select type of variants to use for plotting">
+		<option value="TRUE">SNPs</option>
+		<option value="FALSE">all</option>
+	</param>
+	<when value="TRUE">
+		<param name="true" type="hidden" value="TRUE" label="Use only SNP variants" help=" "/>
+	</when>
+	<when value="FALSE">
+		<param name="false" type="hidden" value="FALSE" label="Use all types of variants" help=" "/>
+	</when>
+	</conditional>
+	
+<param type="float" name="lsp" value="0.4" label="Loess span" help="Parameter that controls the smoothing of the Loess curve"/>
+<param type="text" name="pcol" value="black" label="Colour of scatterplot points" help="See below for list of supported colors"/>
+<param type="text" name="lcol" value="red" label="Colour of Loess curve" help="See below for list of supported colors"/>
+
+
+<conditional name="xaxis">
+	<param name="xaxis_select" type="select" label="Spacing of the x-axis in plots">
+		<option value="TRUE">True</option>
+		<option value="FALSE">False</option>
+	</param>
+	<when value="TRUE">
+		<param name="true" type="hidden" value="TRUE" label="Uniform spacing of the x-axis based on Mb" help="Scale of x-axis (in Mb) is fixed for the scatter plots and frequency plots across all chromosomes"/>
+	</when>
+	<when value="FALSE">
+		<param name="false" type="hidden" value="FALSE" label="Variable spacing of the x-axis based on chromosome lengths" help="Scale of x-axis (in Mb) is dependent on chromosome length for the scatter plots and frequency plots for all chromosomes"/>
+	</when>
+	</conditional>
+
+<param type="integer" name="bsize" value="1000000" label="bin size" help="Size of the bins (in bp) for barplot of frequency of homozygous variants along chromosomes"/>
+
+<conditional name="binnorm">
+	<param name="binnorm_select" type="select" label="Normalisation of y-axis in frequency barplots">
+		<option value="TRUE">True</option>
+		<option value="FALSE">False</option>
+	</param>
+	<when value="TRUE">
+		<param name="true" type="hidden" value="TRUE" label="Normalised y-axis frequency values based on formula" help="Normalisation formula as in cloudmap paper"/>
+	</when>
+	<when value="FALSE">
+		<param name="false" type="hidden" value="FALSE" label="Original frequency y-axis values" help=" "/>
+	</when>
+	</conditional>
+
+<conditional name="exclfiles">
+	<param name="exclfiles_select" type="select" label="Additional exclusion of variants by subtraction">
+		<option value="FALSE">No</option>
+		<option value="TRUE">Yes</option>
+	</param>	
+	<when value="FALSE">
+		<param name="false" type="hidden" value="FALSE" label="No additional variant subtraction" help=""/>
+	</when>
+	<when value="TRUE">
+		<param name="true" type="data" format="tabular" label="Select variant lists to subtract from your history" help="Requires CHR POS DEPTH REF ALT columns- recommend directly using the output table generated by this tool or refer to it for desired format"/>
+	
+	<param type="float" name="exclthr" value="0" label="Filter based on allelic ratio values" help="For filtering variant subtraction lists, only variants above this threshold value will be used for subtraction (e.g. 0 means all variants and 1 means only homozygous variants"/>
+	<param type="text" name="exclcol" value="green" label="Colour of original loess curve (before additional variant subtraction)" help="See below for list of supported colors"/>
+	</when>
+</conditional>	
+	
+</inputs>
+
+<outputs>
+<data name="parn" format="txt"/>
+<data name="outn" format="txt"/>
+<data name="pdfn" format="pdf"/>
+</outputs>
+
+<tests>
+</tests>
+
+<help>
+</help>
+</tool>
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