From 1d855e5a098b7e27c100d94921a0c0d0bb19c5aa Mon Sep 17 00:00:00 2001
From: Jens Preussner <jens.preussner@mpi-bn.mpg.de>
Date: Wed, 4 Mar 2015 12:59:33 +0100
Subject: [PATCH] Added XML definition for galaxy

---
 admire.xml | 106 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 admire.xml

diff --git a/admire.xml b/admire.xml
new file mode 100644
index 0000000..0b1371b
--- /dev/null
+++ b/admire.xml
@@ -0,0 +1,106 @@
+<tool id="admire" name="admire">
+	<requirements>
+		<requirement type="package">anaconda</requirement>
+		<requirement type="package">bedtools</requirement>
+		<requirement type="package">r</requirement>
+		<requirement type="package">comb-p</requirement>
+	</requirements>
+	<description>methylation analysis</description>
+	<command>
+	/home/galaxy/galaxy-dist/tools/admire/src/admire
+	-z /home/galaxy/galaxy-dist/database/files/ftp/$__user_email__/$idat
+	-c $sheet
+	-n $c_norm.normalization
+	-q $fdr
+	-p $det_p
+	-t $s_thresh
+	#if str($i_report) == "create"
+	-e
+	#echo $o_qc#
+	#end if
+	#if $c_norm.normalization == "fn"
+	#echo $c_norm.bgnoob#
+	#echo $c_norm.dyenoob#
+	#end if
+	#if $c_norm.normalization == "noob"
+        #echo $c_norm.dyenoob#
+        #end if
+	#if $c_norm.normalization == "quantile"
+        #echo $c_norm.fixoutliers#
+	#echo $c_norm.removesamples#
+	-l $c_norm.samplecutoff
+        #end if
+	#if str($regions) != "None"
+	#set $r=str($regions).split(",")
+        #for $region in $r
+        #set global $reg=$region
+        -r ${ filter( lambda x: str( x[0] ) == str( $reg ), $__app__.tool_data_tables[ 'admire_regions' ].get_fields() )[0][-1] }
+        #end for
+        #end if
+	#for $custom in $customs
+	-r $custom.cr
+	#end for
+	-o $o_compressed > $o_log
+	</command>
+	<inputs>
+		<param name="idat" type="text" label="Filename of compressed IDAT files" help="Upload compressed IDAT scanner files into your private FTP directory at ftp://bioinformatics.mpi-bn.mpg.de and provide the filename here." />
+		<param name="sheet" type="data" format="txt,csv" label="Sample Sheet from Illumna iScan/HiScan system" help="Provide the CSV file called SampleSheet.csv from the Illumina Scanner."/>
+		<param name="i_report" type="boolean" checked="true" truevalue="create" falsevalue="no" label="Include quality control report in output" help="Quality control might help to identidy failed samples." />
+		<conditional name="c_norm">
+			<param name="normalization" type="select" label="Select a method for input normalization" help="Normalization helps to reduce technical variation between arrays by taking internal controls into account.">
+				<option value="fn" selected="true">Functional normalization</option>
+				<option value="noob">Noob normalization</option>
+				<option value="swan">SWAN normalization</option>
+				<option value="quantile">Quantile normalization</option>
+				<option value="illumina">Illumina Genome Studio normalization</option>
+				<option value="raw">No normalization - use raw values</option>
+			</param>
+			<when value="fn">
+				<param name="bgnoob" type="select" label="Use noob background correction prior to functional normalization">
+                                	<option value="" selected="true">Yes</option>
+                                	<option value="-b">No</option>
+                        	</param>
+				<param name="dyenoob" type="select" label="Use noob dye correction for functional normalization">
+                                        <option value="" selected="true">Yes</option>
+                                        <option value="-d">No</option>
+                                </param>
+			</when>
+			<when value="noob">
+				<param name="dyenoob" type="select" label="Use dye correction for noob normalization">
+                                        <option value="" selected="true">Yes</option>
+                                        <option value="-d">No</option>
+                                </param>
+			</when>
+			<when value="quantile">
+				<param name="fixoutliers" type="select" label="Fix low signal outliers">
+					<option value="" selected="true">Yes</option>
+					<option value="-f">No</option>
+				</param>
+				<param name="samplecutoff" type="float" min="0" value="10.5" label="Bad sample cutoff" help="Label samples as bad if their median signals are below the given value." />
+				<param name="removesamples" type="select" label="Remove samples labelled as bad">
+					<option value="" selected="true">No</option>
+					<option value="-m">Yes</option>
+				</param>
+			</when>
+		</conditional>
+		<param name="det_p" label="Detection p-value threshold for failed probe identification" type="float" min="0" max="1" value="0.01" help="Mark a probes as failed, if it has a detection p-value higher than the given value. Failed probes can be excluded from subsequent analysis using the failed sample threshold (see below)." />
+		<param name="s_thresh" label="Failed sample threshold" type="float" min="0" max="1" value="0.4" help="Probes are excluded from subsequent analysis if the proportion of failed probes across all samples is higher than the given value." />
+		<param name="fdr" label="Q-value cutoff for multiple testing" type="float" min="0" max="1" value="0.05" help="Definde a false discovery rate to limit results after multiple testing correction." />
+		<param name="regions" type="select" label="Select genomic regions to test" display="checkboxes" multiple="true" help="Regions will be overlapped with GC probes and significant different methylated regions will be reported.">
+			<options from_data_table="admire_regions" />
+		</param>
+		<repeat name="customs" title="custom genomic region">
+			<param name="cr" type="data" format="bed" label="Select region" help="Please provide a bed file with hg19 coordinates"/>
+		</repeat>
+	</inputs>
+	<outputs>
+		<data name="o_log" format="txt" label="admire output" /> 
+		<data name="o_compressed" format="tgz" label="compressed output" />
+		<data name="o_qc" format="pdf" label="Quality control report">
+			<filter>i_report==True</filter>
+		</data>
+	</outputs>
+	
+	<help>
+	</help> 
+</tool>