<tool id ="pyReadAligner" name="pyReadAligner">
	<requirements>
			<requirement type="package">pyCRAC</requirement>
		</requirements>
	<command interpreter="python"> 
	/usr/local/bin/pyReadAligner.py
	-f $ftype.input
	--file_type $ftype.file_type
	#if $geneOpt.alignGene == "gene":
		-g $geneOpt.genes
	#end if#
	#if $geneOpt.alignGene == "chr":
		--chr $geneOpt.chr
	#end if#
		#if ($ftype.file_type == "novo" or $ftype.file_type == "sam") and $ftype.disc.discard == "discard":	 
				   --discarded $discarded
		#end if#	   
	--gtf=$addGTF.gtf
	--tab=$addTab.tab
	#if ($ftype.file_type == "novo" or $ftype.file_type == "sam") and $ftype.addAlignOpt.alignoptions == "edit":
		   --align_quality=$ftype.addAlignOpt.align_quality			
		   --align_score=$ftype.addAlignOpt.align_score							
		   --distance=$ftype.addAlignOpt.d									
		   --length=$ftype.addAlignOpt.length	
		   #if int($ftype.addAlignOpt.max) > 0:									
		        --max=$ftype.addAlignOpt.max							 
		   #end if#
		   $ftype.addAlignOpt.unique										   
		   $ftype.addAlignOpt.blocks		   
		   $ftype.addAlignOpt.mutations	 
	#end if#
	#if $addOpt.options == "edit":
		--range=$addOpt.range
		--overlap=$addOpt.overlap
		$addOpt.ignore
		-s $addOpt.sequence
		#if int($addOpt.limit) > 0:
			--limit=$addOpt.limit
		#end if#
	#end if#
	-o $output	
	</command>
	<version_command>/usr/local/bin/pyReadAligner.py --version</version_command>
	<inputs>


			<conditional name="geneOpt">
						<param name="alignGene" type="select"  label="Do you want to align reads to genes or chromosome co-ordinates?">
								<option value="gene" selected="true">Genes</option>
								<option value="chr">Chromosome Co-ordinates</option>
						</param>
						<when value="chr">
			  <param format="interval" name="chr" type="data" label="Choose a Chromosome Coordinate File" help="Tab delimited text file contai\
ning an identifier, chromosome name, start position, end position and strand ('-' or '+')"/>
						</when>
						<when value="gene">
			  <param format="txt" name="genes" type="data" label="Choose a Gene List -g" help="Single column gene ID file"/>
						</when>
		</conditional>
				<conditional name="addGTF">
						<param name="gtfFile" type="select"	 label="Choose GTF File from">
								<option value="default" selected="true">Defaults</option>
								<option value="other">History</option>
						</param>
						<when value="default">
								<param name="gtf" type="select"	 label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
										<options from_data_table="pycrac_gtf"/>
								</param>
						</when>
						<when value="other">
								<param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
						</when>
				</conditional>
			   <conditional name="addTab">
						<param name="tabFile" type="select"	 label="Choose Genomic Reference Sequence from">
								<option value="default" selected="true">Defaults</option>
								<option value="other">History</option>
						</param>
						<when value="default">
								<param name="tab" type="select"	 label="Genomic Reference Sequence --tab" help="Tab file containing genomic reference sequence">
										<options from_data_table="pycrac_tab"/>
								</param>
						</when>
						<when value="other">
								<param format="tabular" name="tab" type="data" label="Genomic Reference Sequence --tab" help="Tab file containing genomic reference sequence"/>
						</when>
		   </conditional>


		<conditional name="ftype">
			<param name="file_type" type="select"  label="Input File Type --file_type">
					<option value="sam">Sam/BAM</option>
					<option value="novo">Novo</option>
					<option value="gtf">GTF</option>
			</param>
			<when value="sam">
				<param format="sam,bam" name="input" type="data" label="Input File -f" help="Alignment file of type .sam or .bam"/>
				<conditional name="disc">
				  <param name="discard" type="select"  label="Print discarded reads to a separate file">
				<option value="" selected="true">OFF</option>
				<option value="discard">ON</option>
				  </param>
				  <when value="discard">
				  </when>
				  <when value="">
				  </when>
				</conditional>
				<conditional name="addAlignOpt">
				<param name="alignoptions" type="select"  label="Alignment Options">
									<option value="default" selected="true">Default</option>
									<option value="edit">Edit</option>
								</param>
								<when value="edit">
									<param name="mutations" type="select"  label="Filter reads by mutations --mutations" help="cross-linking sites are often highlighted by deletions and/or substitutions in the reads. You can use this option to filter reads based on whether they have mutations or not.">
									  <option value="" selected="true">Off</option>
									  <option value="--mutations=delsonly">deletions</option>
									  <option value="--mutations=subsonly">substitutions</option>
									  <option value="--mutations=TC">T->C mutations</option>
									  <option value="--mutations=allmuts">all mutations</option>
									  <option value="--mutations=nomuts">no mutations</option>
									</param>
									<param format="integer" name="align_quality" type="integer" label="Align Quality --align_quality " value="0" size="5" >
									  <validator type="in_range" min="0" message="Please enter a value >= 0"/>
									</param>
									<param format="integer" name="align_score" type="integer" label="Align Score --align_score " value="0" size="5" >
									  <validator type="in_range" min="0" message="Please enter a value >= 0"/>
									</param>
									<param format="integer" name="max" type="integer" label="Mapped reads to read from input file --max" help="Set to 0 to align all reads." value="0" size="10" >
									  <validator type="in_range" min="0" max="100000000" message="Please enter a value between 1 and 100000000 or 0 to align all reads"/>
									</param>
									<param format="integer" name="d" type="integer" label="Distance --distance " value="1000" size="6" help="Set the maximum number of bp allowed between two non-overlapping paired reads">
									  <validator type="in_range" min="1" message="Please enter a value >= 0"/>
									</param>
									<param format="integer" name="length" type="integer" label="Set the maximum length of reads --length" value="1000" size="7" help="Set the read length threshold between 15 and 1000">
									  <validator type="in_range" min="15" max="1000" message="Please enter a value between 15 and 1000"/>
									</param>
									<param name="unique" type="select"	label="Remove reads with multiple alignment locations --unique">
									  <option value="" selected="true">OFF</option>
									  <option value="--unique">ON</option>
									</param>
									<param name="blocks" type="select"	label="Only count reads with same start and end coords once --blocks">
									  <option value="" selected="true">OFF</option>
									  <option value="--blocks">ON</option>
									</param>
								</when>
								<when value="default">
								</when>
				</conditional>
			</when>
			<when value="novo">
				<param format="tabular" name="input" type="data" label="Input File -f" help="Alignment file of type .novo" />
				<conditional name="disc">
				  <param name="discard" type="select"  label="Print discarded reads to a separate file">
					<option value="" selected="true">OFF</option>
					<option value="discard">ON</option>
				  </param>
				  <when value="discard">
				  </when>
				  <when value="">
				  </when>
				</conditional>
								<conditional name="addAlignOpt">
								<param name="alignoptions" type="select"  label="Alignment Options">
									<option value="default" selected="true">Default</option>
									<option value="edit">Edit</option>
								</param>
								<when value="edit">
									<param name="mutations" type="select"  label="Filter reads by mutations --mutations" help="cross-linking sites are often
 highlighted by deletions and/or substitutions in the reads. You can use this option to filter reads based on whether they have mutations or not.">
									  <option value="" selected="true">Off</option>
									  <option value="--mutations=delsonly">deletions</option>
									  <option value="--mutations=subsonly">substitutions</option>
									  <option value="--mutations=TC">T->C mutations</option>
									  <option value="--mutations=allmuts">all mutations</option>
									  <option value="--mutations=nomuts">no mutations</option>
									</param>
									<param format="integer" name="align_quality" type="integer" label="Align Quality --align_quality " value="0" size="5" >
									  <validator type="in_range" min="0" message="Please enter a value >= 0"/>
									</param>
									<param format="integer" name="align_score" type="integer" label="Align Score --align_score " value="0" size="5" >
									  <validator type="in_range" min="0" message="Please enter a value >= 0"/>
									</param>
									<param format="integer" name="max" type="integer" label="Mapped reads to read from input file --max" help="Set to 0 to align all reads." value="0" size="10" >
									  <validator type="in_range" min="0" max="100000000" message="Please enter a value between 1 and 100000000 or 0 to align all reads"/>
									</param>
									<param format="integer" name="d" type="integer" label="Distance --distance " value="1000" size="6" help="Set the maximum number of bp allowed between two non-overlapping paired reads">
									  <validator type="in_range" min="1" message="Please enter a value >= 0"/>
									</param>
									<param format="integer" name="length" type="integer" label="Set the maximum length of reads --length" value="1000" size="7" help="Set the read length threshold between 15 and 1000">
									  <validator type="in_range" min="15" max="1000" message="Please enter a value between 15 and 1000"/>
									</param>
									<param name="unique" type="select"	label="Remove reads with multiple alignment locations --unique">
									  <option value="" selected="true">OFF</option>
									  <option value="--unique">ON</option>
									</param>
									<param name="blocks" type="select"	label="Only count reads with same start and end coords once --blocks">
									  <option value="" selected="true">OFF</option>
									  <option value="--blocks">ON</option>
									</param>
								</when>
								<when value="default">
								</when>
			</conditional>
			</when>
			<when value="gtf">
				<param format="gtf" name="input" type="data" label="Input File -f" help="File of type .gtf" />
			</when>
			  </conditional>
			  
			  <conditional name="addOpt">
			<param name="options" type="select"	 label="Standard Options">
			  <option value="default" selected="true">Default</option>
			  <option value="edit">Edit</option>
			</param>		
			<when value="edit">
			  <param format="integer" name="range" type="integer" label="Range --range" value="0" size="5" help="Manually set the length of the 5' and 3' UTRs 0>50000">
				<validator type="in_range" min="0" max="50000" message="Please enter a value between 0 and 50000"/>
			  </param>
			  <param name="ignore" type="select" label="Ignore strand information? --ignorestrand">
				<option value="" selected="true">No</option>
				<option value="--ignorestrand">Yes</option>
			  </param>
			  <param format="integer" name="overlap" type="integer" label="Overlap --overlap" value="1" size="5" help="Sets the number of nucleotides a read has to overlap with a gene before it is considered a hit. ">
				<validator type="in_range" min="1" message="Please enter a positive integer"/>
			  </param>
						  <param name="sequence" type="select" label="Align reads to --sequence">
							<option value="genomic" selected="true">Genomic Sequence</option>
							<option value="coding">Coding Sequence</option>
						  </param>
			  <param format="integer" name="limit" type="integer" label="Limit number of reads to count that map to a particular region --limit" value="0" size="15" help="Set to 0 for unlimited reads" >
				<validator type="in_range" min="0" message="Please enter a value greater than 1 or set to 0 for unlimited reads"/>
			  </param> 
			</when>
			<when value="default">
			</when>
			  </conditional>
				<param name="label" type="text" format="txt" size="30" value="pyReadAligner" label="Enter output file label -o" />
	</inputs>
	<outputs>
		<data format="fasta" name="output" label="${label.value}.aligned.fasta"/>
				<data format="txt" name="discarded" label="${label.value}_discarded.txt">
						<filter>(ftype['file_type'] == "novo" or ftype['file_type'] == "sam") and ftype['disc']['discard'] ==  "discard"</filter>
				</data> 
	</outputs>
	<help>


.. class:: infomark

**pyReadAligner**

pyReadAligner is part of the pyCRAC_ package. Generates multiple sequence alignments for reads mapped to individual genes or genomic regions. 
Produces a fasta output file.

   
.. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
		
------

**Parameter list**

File input options::

	-f FILE, --input_file=FILE
						As input files you can use Novoalign native output or
						SAM files as input file. By default it expects data
						from the standard input. Make sure to specify the file
						type of the file you want to have analyzed using the
						--file_type option!
	-o OUTPUT_FILE, --output_file=OUTPUT_FILE
						Use this flag to override the standard output file
						names. All alignments will be written to one output
						file.
	-g FILE, --genes_file=FILE
						here you need to type in the name of your gene list
						file (1 column) or the hittable file
	--chr=FILE			
                                                if you simply would like to align reads against a
						genomic sequence you should generate a tab delimited
						file containing an identifyer, chromosome name, start
						position, end position and strand
	--gtf=annotation_file.gtf
						type the path to the gtf annotation file that you want
						to use
	--tab=tab_file.tab	
                                                type the path to the tab file that contains the
						genomic reference sequence
	--file_type=FILE_TYPE
						use this option to specify the file type (i.e. 'novo',
						'sam', 'gtf'). This will tell the program which
						parsers to use for processing the files. Default =
						'novo'

pyReadAligner specific options::

	--limit=500			
                                                with this option you can select how many reads mapped
						to a particular gene/ORF/region you want to count.
						Default = All

Common options::

	--ignorestrand		
                                                this flag tells the program to ignore strand
						information and all overlapping reads will considered
						sense reads. Useful for analysing ChIP or RIP data
	--overlap=1			
                                                sets the number of nucleotides a read has to overlap
						with a gene before it is considered a hit. Default =
						1 nucleotide
	-s genomic, --sequence=genomic
						with this option you can select whether you want the
						reads aligned to the genomic or the coding sequence.
						Default = genomic
	-r 100, --range=100
						allows you to set the length of the UTR regions. If
						you set '-r 50' or '--range=50', then the program will
						set a fixed length (50 bp) regardless of whether the
						GTF file has genes with annotated UTRs.

Options for novo, SAM and BAM files::

	--align_quality=100, --mapping_quality=100
						with these options you can set the alignment quality
						(Novoalign) or mapping quality (SAM) threshold. Reads
						with qualities lower than the threshold will be
						ignored. Default = 0
	--align_score=100	
                                                with this option you can set the alignment score
						threshold. Reads with alignment scores lower than the
						threshold will be ignored. Default = 0
	-l 100, --length=100
						to set read length threshold. Default = 1000
	-m 100000, --max=100000
						maximum number of mapped reads that will be analyzed.
						Default = All
	--unique			      
                                                with this option reads with multiple alignment
						locations will be removed. Default = Off
	--blocks			
                                                with this option reads with the same start and end
						coordinates on a chromosome will only be counted once.
						Default = Off
	--discarded=FILE	                
                                                prints the lines from the alignments file that were
						discarded by the parsers. This file contains reads
						that were unmapped (NM), of poor quality (i.e. QC) or
						paired reads that were mapped to different chromosomal
						locations or were too far apart on the same
						chromosome. Useful for debugging purposes
	-d 1000, --distance=1000
						this option allows you to set the maximum number of
						base-pairs allowed between two non-overlapping paired
						reads. Default = 1000
	--mutations=delsonly
						Use this option to only track mutations that are of
						interest. For CRAC data this is usually deletions
						(--mutations=delsonly). For PAR-CLIP data this is
						usually T-C mutations (--mutations=TC). Other options
						are: do not report any mutations: --mutations=nomuts.
						Only report specific base mutations, for example only
						in T's, C's and G's :--mutations=[TCG]. The brackets
						are essential. Other nucleotide combinations are also
						possible


	</help>
</tool>