Mercurial > repos > drosofff > msp_sr_signature
changeset 5:71a3992ef132 draft
Deleted selected files
| author | drosofff |
|---|---|
| date | Thu, 21 May 2015 10:36:43 -0400 |
| parents | 741cc1d16813 |
| children | d2a220e64a1c |
| files | signature.xml~ |
| diffstat | 1 files changed, 0 insertions(+), 148 deletions(-) [+] |
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--- a/signature.xml~ Thu Apr 16 05:45:19 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,148 +0,0 @@ -<tool id="signature" name="Small RNA Signatures" version="2.0.1"> - <description /> - <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> - <requirement type="package" version="0.7.7">pysam</requirement> - <requirement type="package" version="2.14">biocbasics</requirement> - <requirement type="package" version="3.0.3">R</requirement> - <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="0.14">scipy</requirement> - </requirements> - <command interpreter="python"> - signature.py - --input $refGenomeSource.input - --inputFormat $refGenomeSource.input.ext - --minquery $minquery - --maxquery $maxquery - --mintarget $mintarget - --maxtarget $maxtarget - --minscope $minscope - --maxscope $maxscope - --outputOverlapDataframe $output - #if $refGenomeSource.genomeSource == "history": - --referenceGenome $refGenomeSource.ownFile - #else: - #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] - --referenceGenome $reference - --extract_index - #end if - --graph $graph_type - --rcode $sigplotter - </command> - <inputs> - <conditional name="refGenomeSource"> - <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data"> - <validator message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history." metadata_column="0" metadata_name="dbkey" table_name="bowtie_indexes" type="dataset_metadata_in_data_table" /> - </param> - </when> - <when value="history"> - <param format="fasta" label="Select the fasta reference" name="ownFile" type="data" /> - <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data" /> - </when> - </conditional> - <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" /> - <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" /> - <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" /> - <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" /> - <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" /> - <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" /> - <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="graph_type" type="select"> - <option selected="True" value="global">Global</option> - <option value="lattice">Lattice</option> - </param> - </inputs> - <outputs> - <data format="tabular" label="signature data frame" name="output" /> - <data format="pdf" label="Overlap probabilities" name="output2" /> - </outputs> - <tests> - <test> - <param name="genomeSource" value="history" /> - <param ftype="fasta" name="ownFile" value="ensembl.fa" /> - <param ftype="bam" name="input" value="sr_bowtie.bam" /> - <param name="minquery" value="23" /> - <param name="maxquery" value="29" /> - <param name="mintarget" value="23" /> - <param name="maxtarget" value="29" /> - <param name="minscope" value="5" /> - <param name="maxscope" value="15" /> - <param name="graph_type" value="global" /> - <output file="signature.tab" ftype="tabular" name="output" /> - <output file="signature.pdf" ftype="pdf" name="output2" /> - </test> - </tests> - <help> - -**What it does** - -This tool computes the number of pairs by overlap classes (in nt) from a bowtie output file, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science. -The numerical options set the min and max size of both the query small rna class and the target small rna class. -Three type of signals are plotted in separate pdf files, the number of pairs founds, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science. - - </help> - <citations> - <citation type="doi">10.1007/978-1-4939-0931-5_12</citation> - </citations> - <configfiles> - <configfile name="sigplotter"> - graph_type = "${graph_type}" - - globalgraph = function () { - ## Setup R error handling to go to stderr - options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) - signature = read.delim("${output}", header=TRUE) - signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2])) - overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3])) - YLIM=max(signature[,2]) - - ## Open output2 PDF file - pdf( "${output2}" ) - par(mfrow=c(2,2),oma = c(0, 0, 3, 0)) - - plot(signature[,1:2], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylim=c(0,YLIM), ylab="Numbers of pairs", col="darkslateblue", lwd=4) - - plot(signaturez, type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) - - plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities", - cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50), - pch=19, col="darkslateblue", lwd=2) - - plot(overlap_prob_z, type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2) - - mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1) - devname = dev.off() - ## Close the PDF file - } - - treillisgraph = function () { - ## Open output2 PDF file - pdf( "${output2}", paper="special", height=11.69, width=8.2677 ) - signature = read.delim("${output}", header=TRUE) - options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) - library(lattice) - print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(${minscope},${maxscope}), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", - par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5), - cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]", - pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2, - layout=c(4,12), as.table=TRUE, newpage = T) ) - devnname = dev.off() - } - - if (graph_type=="global") { - globalgraph() - - } - if(graph_type=="lattice") { - treillisgraph() - } - </configfile> - </configfiles> -</tool>