Mercurial > repos > crs4 > exomedepth

changeset 7:45af4a9748cf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth commit 91a0182476a7fc26be7bef1677790518c4e88348"
author iuc
date Fri, 08 Nov 2019 13:25:44 -0500
parents 165732ee5a48
children 5d60331757d3
files exomedepth-a9701c421408/exomedepth.R exomedepth.R exomedepth.xml test-data/CNV_TruSeq_Chr2.bed test-data/CNV_case_small.bam test-data/CNV_control_small.bam
diffstat 6 files changed, 810 insertions(+), 157 deletions(-) [+]
line wrap: on
line diff
--- a/exomedepth-a9701c421408/exomedepth.R	Mon Jun 11 09:34:25 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-# Load ExomeDepth library (without warnings)
-suppressMessages(library(ExomeDepth))
-
-# Import parameters from xml wrapper (args_file)
-args  <- commandArgs(trailingOnly=TRUE)
-param <- read.table(args[1],sep="=", as.is=TRUE)
-
-# Set common parameters
-target      <- param[match("target",param[,1]),2]
-trans_prob  <- as.numeric(param[match("trans_prob",param[,1]),2])
-output      <- param[match("output",param[,1]),2]
-test_vs_ref <- as.logical(param[match("test_vs_ref",param[,1]),2])
-
-# Create symbolic links for multiple bam and bai 
-bam         <- param[param[,1]=="bam",2]
-bam_bai     <- param[param[,1]=="bam_bai",2]
-bam_label   <- param[param[,1]=="bam_label",2]
-bam_label   <- gsub(" ", "_", bam_label)
-
-for(i in 1:length(bam)){
-  stopifnot(file.symlink(bam[i], paste(bam_label[i], "bam", sep=".")))
-  stopifnot(file.symlink(bam_bai[i], paste(bam_label[i], "bam.bai", sep=".")))
-}
-
-# Generate read count data
-BAMFiles <- paste(bam_label, "bam", sep=".")
-sink("/dev/null")
-ExomeCount <- suppressMessages(getBamCounts(bed.file=target, bam.files = BAMFiles))
-sink()
-
-# Convert counts in a data frame
-ExomeCount.dafr <- as(ExomeCount[, colnames(ExomeCount)], 'data.frame')
-
-# Prepare the main matrix of read count data
-ExomeCount.mat <- as.matrix(ExomeCount.dafr[, grep(names(ExomeCount.dafr), pattern='.bam')])
-
-# Remove .bam from sample name
-colnames(ExomeCount.mat) <- gsub(".bam", "", colnames(ExomeCount.mat))
-
-# Set nsamples == 1 if mode is test vs reference, assuming test is sample 1
-nsamples <- ifelse(test_vs_ref, 1, ncol(ExomeCount.mat))
-
-# Loop over samples
-for (i in 1:nsamples){
-
-	# Create the aggregate reference set for this sample
-	my.choice <- suppressWarnings(suppressMessages(
-					select.reference.set(test.counts = ExomeCount.mat[,i],  
-                           				 reference.counts = subset(ExomeCount.mat, select=-i),  
-                           			     bin.length = (ExomeCount.dafr$end - ExomeCount.dafr$start)/1000,
-                           		         n.bins.reduced = 10000)))
-
-	my.reference.selected <- apply(X = ExomeCount.mat[, my.choice$reference.choice, drop=FALSE],
-                               	   MAR = 1,
-                               	   FUN = sum)
-                               
-	# Now create the ExomeDepth object for the CNVs call
-	all.exons<-suppressWarnings(suppressMessages(new('ExomeDepth',
-               test = ExomeCount.mat[,i],
-               reference = my.reference.selected,
-               formula = 'cbind(test,reference)~1')))
-
-
-	# Now call the CNVs
-	result <- try(all.exons<-suppressMessages(CallCNVs(x=all.exons,
-                            transition.probability = trans_prob,
-                            chromosome = ExomeCount.dafr$space,
-                            start = ExomeCount.dafr$start,
-                            end = ExomeCount.dafr$end,
-                            name = ExomeCount.dafr$names)), silent=T)
-
-	# Next if CNVs are not detected
-	if (class(result)=="try-error"){
-		next
-	}
-
-	# Compute correlation between ref and test
-	my.cor <- cor(all.exons@reference, all.exons@test)
-	n.call <- nrow(all.exons@CNV.calls)
-
-	# Write results
-	my.results <- cbind(all.exons@CNV.calls[,c(7,5,6,3)], 
-            		 	sample=colnames(ExomeCount.mat)[i],
-            			corr=my.cor,
-            			all.exons@CNV.calls[,c(4,9,12)])
-            			
-    	# Re-order by chr and position
-    	chrOrder<-c(paste("chr",1:22,sep=""),"chrX","chrY","chrM")
-    	my.results[,1] <- factor(my.results[,1], levels=chrOrder)
-    	my.results <- my.results[order(my.results[,1], my.results[,2], my.results[,3]),]
-    
-	write.table(sep='\t', quote=FALSE, file = output,
-            		x = my.results,
-       			row.names = FALSE, col.names = FALSE, dec=".", append=TRUE)
-}
--- a/exomedepth.R	Mon Jun 11 09:34:25 2018 -0400
+++ b/exomedepth.R	Fri Nov 08 13:25:44 2019 -0500
@@ -3,8 +3,7 @@
 
 # Import parameters from xml wrapper (args_file)
 args  <- commandArgs(trailingOnly=TRUE)
-eval(parse(text=args[[1]]))
-param <- read.table(mypars,sep="=", as.is=TRUE)
+param <- read.table(args[1],sep="=", as.is=TRUE)
 
 # Set common parameters
 target      <- param[match("target",param[,1]),2]
--- a/exomedepth.xml	Mon Jun 11 09:34:25 2018 -0400
+++ b/exomedepth.xml	Fri Nov 08 13:25:44 2019 -0500
@@ -1,31 +1,17 @@
-<tool id="exomedepth" name="ExomeDepth" version="1.0.0">
-  <description>cnv caller</description>
-  <requirements>
-	  <requirement type="package" version="1.1.10">r-exomedepth</requirement>
-  </requirements>
-  <command>
-    R CMD BATCH --no-save --no-restore '--args mypars="$args_file"' $__tool_directory__/exomedepth.R
-  </command>
-  <inputs>
-    <param format="bed" name="targetFile" type="data" label="Target regions (BED)">
-      <validator type="unspecified_build" />
-    </param>
-    <param name="test_vs_ref" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Call CNVs using 1st sample as test" help="If checked, the tool will call CNVs in the first sample vs all the others. If unchecked, an all vs all CNV call will be performed" />
-    <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
-      <param format="bam" name="input" type="data" label="BAM file">
-        <options>
-          <filter type="data_meta" ref="targetFile" key="dbkey"/>
-        </options>
-      </param>
-      <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
-           <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
-      </param>  
-    </repeat>
-    <param name="transition_probability" size="10" type="float" value="0.0001" label="Transition probability" help="Transition probability of the hidden Markov Chain from the normal copy number state to either a deletion or a duplication. The default value (0.0001) expects approximately 20 CNVs genome-wide" />
-  </inputs>
-
-  <configfiles>
-    <configfile name="args_file">target=$targetFile
+<tool id="exomedepth" name="ExomeDepth" version="1.1.0">
+    <description>Calls copy number variants (CNVs) from targeted sequence data</description>
+    <requirements>
+        <requirement type="package" version="1.1.10">r-exomedepth</requirement>
+    </requirements>
+    <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", ExomeDepth version" $(R --vanilla --slave -e "library(ExomeDepth); cat(sessionInfo()\$otherPkgs\$ExomeDepth\$Version)")
+    ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript '${__tool_directory__}/exomedepth.R' '$args_file'
+    ]]></command>
+    <configfiles>
+        <configfile name="args_file"><![CDATA[
+target=$targetFile
 test_vs_ref=$test_vs_ref
 #for $i in $inputs
 bam=${i.input}
@@ -38,13 +24,51 @@
 #end for
 trans_prob=$transition_probability
 output=$output
-</configfile>
-  </configfiles>
-  <outputs>
-    <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
-  </outputs>
-  <help>
-
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="targetFile" type="data" format="bed" label="Target regions (BED)">
+            <validator type="unspecified_build" />
+        </param>
+        <param name="test_vs_ref" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Call CNVs using 1st sample as test" help="If checked, the tool will call CNVs in the first sample vs all the others. If unchecked, an all vs all CNV call will be performed" />
+        <repeat name="inputs" title="BAM" min="2" help="Need to add more files? Use controls below.">
+            <param name="input" type="data" format="bam" label="BAM file">
+                <options>
+                    <filter type="data_meta" ref="targetFile" key="dbkey"/>
+                </options>
+            </param>
+            <param name="label" type="text" size="30" value="" label="Label" help="Label to use in the output. If not given, the dataset name will be used instead">
+                <validator type="regex" message="Spaces are not allowed">^\S*$</validator>
+            </param>  
+        </repeat>
+        <param name="transition_probability" size="10" type="float" value="0.0001" label="Transition probability" help="Transition probability of the hidden Markov Chain from the normal copy number state to either a deletion or a duplication. The default value (0.0001) expects approximately 20 CNVs genome-wide" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="targetFile" value="CNV_TruSeq_Chr2.bed" dbkey="hg19" ftype="bed"/>
+            <param name="test_vs_ref" value="True"/>
+            <repeat name="inputs">
+                <param name="input" value="CNV_case_small.bam"/>
+            </repeat>
+            <repeat name="inputs">
+                <param name="input" value="CNV_control_small.bam"/>
+            </repeat>
+            <param name="transition_probability" value="0.5"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="chr2" />
+                    <has_text text="97890544" />
+                    <has_text text="97890616" />
+                    <has_text text="deletion" />
+                    <has_text text="CNV_case_small" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
 .. class:: warningmark
 
 **Warning about counts for chromosome X**
@@ -92,30 +116,9 @@
 (at least 20 genes, say, but probably more would be useful). Also note that PCR based enrichment studies are often 
 not well suited for this type of read depth analysis. The reason is that as the number of cycles is often set to a high 
 number in order to equalize the representation of each amplicon, which can discard the CNV information.
-
-**License and citation**
-
-This Galaxy tool is Copyright © 2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
-
-.. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
-
-You can use this tool only if you agree to the license terms of: `ExomeDepth`_.
-
-.. _ExomeDepth: http://cran.r-project.org/web/packages/ExomeDepth/
-
-If you use this tool, please cite:
-
-- |Cuccuru2014|_
-- |Plagnol2012|_.
-
-.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
-.. |Plagnol2012| replace:: Plagnol, V., *et al.* (2012) A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. *Bioinformatics* 28(21), 2747-2754
-.. _Plagnol2012: http://bioinformatics.oxfordjournals.org/content/28/21/2747
-  </help>
+    ]]></help>
     <citations>
-    <citation type="doi">10.1093/bioinformatics/btu135</citation>
-    <citation type="doi">10.1093/bioinformatics/bts526</citation>
-  </citations>
+        <citation type="doi">10.1093/bioinformatics/btu135</citation>
+        <citation type="doi">10.1093/bioinformatics/bts526</citation>
+    </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/CNV_TruSeq_Chr2.bed	Fri Nov 08 13:25:44 2019 -0500
@@ -0,0 +1,746 @@
+chr2	91824709	91825059	LOC654342
+chr2	91842946	91843023	LOC654342
+chr2	91843394	91843528	LOC654342
+chr2	91963368	91964133	GGT8P
+chr2	91968436	91970153	GGT8P
+chr2	92129159	92130494	FKSG73
+chr2	95426675	95426777	ANKRD20B
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+chr2	95456835	95456888	ANKRD20B
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+chr2	99224770	99224955	C2orf64
+chr2	99225042	99225189	UNC50
+chr2	99226219	99226502	UNC50
+chr2	99227238	99227358	UNC50
+chr2	99232670	99232809	UNC50
+chr2	99232895	99232996	UNC50
+chr2	99234631	99234975	UNC50
+chr2	99235571	99237968	MGAT4A
+chr2	99242186	99242298	MGAT4A
+chr2	99251685	99251751	MGAT4A
+chr2	99252980	99253058	MGAT4A
+chr2	99256271	99256464	MGAT4A
+chr2	99256584	99256691	MGAT4A
+chr2	99260386	99260516	MGAT4A
+chr2	99261891	99262005	MGAT4A
+chr2	99271908	99271983	MGAT4A
+chr2	99272815	99272928	MGAT4A
+chr2	99274681	99274727	MGAT4A
+chr2	99279509	99279642	MGAT4A
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+chr2	99291498	99291638	MGAT4A
+chr2	99294767	99294934	MGAT4A
+chr2	99342702	99343030	MGAT4A
+chr2	99410309	99411134	C2orf55
+chr2	99412583	99412727	C2orf55
+chr2	99413813	99414000	C2orf55
+chr2	99438320	99440000	C2orf55
+chr2	99443438	99443632	C2orf55
+chr2	99448811	99448975	C2orf55
+chr2	99449325	99449460	C2orf55
+chr2	99454582	99454750	C2orf55
+chr2	99463194	99463273	C2orf55
+chr2	99552401	99552684	C2orf55
+chr2	99613725	99614684	TSGA10
+chr2	99634663	99634812	TSGA10
+chr2	99634999	99635103	TSGA10
+chr2	99636743	99636945	TSGA10
+chr2	99651693	99651902	TSGA10
+chr2	99681402	99681587	TSGA10
+chr2	99685351	99685461	TSGA10
+chr2	99688169	99688337	TSGA10
+chr2	99689481	99689536	TSGA10
+chr2	99695122	99695276	TSGA10
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+chr2	99720430	99720581	TSGA10
+chr2	99721822	99721899	TSGA10
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+chr2	99725296	99725454	TSGA10
+chr2	99725852	99725975	TSGA10
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+chr2	99734007	99734222	TSGA10
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+chr2	99758185	99758400	C2orf15
+chr2	99758748	99758864	C2orf15
+chr2	99763865	99763956	C2orf15
+chr2	99766946	99767926	C2orf15
+chr2	99771156	99771187	TSGA10
+chr2	99771418	99771514	LIPT1
+chr2	99771945	99772007	LIPT1
+chr2	99773190	99773317	LIPT1
+chr2	99778420	99779611	LIPT1
+chr2	99785726	99785933	MITD1
+chr2	99786013	99786073	MITD1
+chr2	99787000	99787115	MITD1
+chr2	99787806	99787892	MITD1
+chr2	99787973	99788109	MITD1
+chr2	99790378	99790479	MITD1
+chr2	99797294	99797492	MITD1
+chr2	99797578	99797712	MRPL30
+chr2	99802640	99802717	MRPL30
+chr2	99804640	99804720	MRPL30
+chr2	99811214	99811360	MRPL30
+chr2	99811579	99811652	MRPL30
+chr2	99812036	99814088	MRPL30
+chr2	99858711	99858945	LYG2
+chr2	99860462	99860600	LYG2
+chr2	99861725	99861921	LYG2
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+chr2	99907700	99907884	LYG1
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+chr2	99914922	99915012	LYG1
+chr2	99917513	99917639	LYG1
+chr2	99935489	99936262	TXNDC9
+chr2	99938418	99938672	TXNDC9
+chr2	99943998	99944116	TXNDC9
+chr2	99949485	99949705	TXNDC9
+chr2	99952702	99952860	TXNDC9
+chr2	99953834	99954052	EIF5B
+chr2	99976699	99976824	EIF5B
+chr2	99976928	99977012	EIF5B
+chr2	99977611	99978283	EIF5B
+chr2	99980108	99980325	EIF5B
+chr2	99980734	99980884	EIF5B
+chr2	99984956	99985054	EIF5B
+chr2	99985855	99985944	EIF5B
+chr2	99988119	99988193	EIF5B
+chr2	99992810	99993099	EIF5B
+chr2	99995482	99995589	EIF5B
+chr2	99995781	99995891	EIF5B
+chr2	99998622	99998689	EIF5B
+chr2	99999243	99999384	EIF5B
Binary file test-data/CNV_case_small.bam has changed
Binary file test-data/CNV_control_small.bam has changed