Mercurial > repos > swebb > pycrac
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyCRAC/pyPileup.xml Tue Jun 18 09:11:00 2013 -0400 @@ -0,0 +1,384 @@ +<?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>