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view pyCRAC/pyPileup.xml @ 0:19b20927172d draft
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| author | swebb |
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| date | Tue, 18 Jun 2013 09:11:00 -0400 |
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<?xml version="1.0" encoding="utf-8"?> <tool id ="pyPileup" name="pyPileup"> <requirements> <requirement type="package">pyCRAC</requirement> </requirements> <command interpreter="python"> /usr/local/bin/pyPileup.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 #if $ftype.disc.discard == "--discarded": --discarded $discarded #end if# #end if# #if $addOpt.options == "edit": --range=$addOpt.range --overlap=$addOpt.overlap $addOpt.iclip $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/pyPileup.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 containing 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="novo" selected="true">Novo</option> <option value="sam">Sam/BAM</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 name="iclip" type="select" label="iCLIP mode --iCLIP"> <option value="" selected="true">OFF</option> <option value="--iCLIP">ON</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="pyPileup" label="Enter output file label -o" /> </inputs> <outputs> <data format="tabular" name="output" label="${label.value}.pileup"/> <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 **pyPileup** pyPileup is part of the pyCRAC_ package. Produces pileups containing the number of hits, substitutions and deletions for each nucleotide covered by reads in specific genes or genomic regions .. _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, SAM, pyMotif or pyReadCounters GTF 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 pileups 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' pyPileup 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 --iCLIP This turns on the iCLIP mode and the pileups will report cross-linking site frequencies in iCLIP data in reference sequences Common options:: -v, --verbose prints all the status messages to a file rather than the standard output --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 --zip=FILE use this option to compress all the output files in a single zip file --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>