Mercurial > repos > erasmus-medical-center > voom_transform

changeset 0:c6a3a93a237e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
author erasmus-medical-center
date Wed, 25 Jan 2017 10:13:10 -0500
parents
children
files test-data/em.txt test-data/em_transformed.txt voom_transform.R voom_transform.xml
diffstat 4 files changed, 141 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/em.txt	Wed Jan 25 10:13:10 2017 -0500
@@ -0,0 +1,24 @@
+Geneid	s01	s02	s03	s04	s05	s06	s07	s08	s09	s10	s11	s12	s13	s14	s15	s16
+GENE_0000096	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0000291	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0000382	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0000775	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0001482	1	3	1	1	4	0	0	0	1	0	1	4	2	4	2	4
+GENE_0001809	0	1	3	0	0	0	0	1	1	1	1	1	0	1	0	0
+GENE_0001844	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0002231	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0002319	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0002401	0	0	6	1	3	2	0	0	0	1	2	5	5	0	3	0
+GENE_0002494	6	3	0	1	1	2	1	2	3	0	2	0	3	7	2	3
+GENE_0002571	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0003914	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0003940	438	383	277	365	310	252	195	238	660	554	427	313	351	369	382	572
+GENE_0004029	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+GENE_0004039	50	66	43	44	28	57	14	46	31	43	52	42	34	23	35	79
+GENE_0004049	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
+GENE_0004059	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
+GENE_0004069	1	1	1	0	0	0	0	0	0	0	0	0	0	2	1	0
+GENE_0004079	11	11	8	8	16	8	5	11	13	16	7	7	6	4	7	9
+GENE_0004089	171	198	79	136	171	134	112	89	141	173	126	94	116	151	199	153
+GENE_0004099	286	349	203	274	319	248	254	288	297	253	235	279	227	208	286	207
+GENE_0004111	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/em_transformed.txt	Wed Jan 25 10:13:10 2017 -0500
@@ -0,0 +1,24 @@
+	s01	s02	s03	s04	s05	s06	s07	s08	s09	s10	s11	s12	s13	s14	s15	s16
+GENE_0000096	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0000291	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0000382	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0000775	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0001482	10.6021459378899	11.7502388046096	11.2357602999147	10.817826403275	12.3650916394482	9.47213695068688	9.74669322641589	9.52855654574918	10.3516241433696	8.90642900704567	10.7784388104248	12.5584617505112	11.712400048862	12.5109065208515	11.4111463207977	12.0958690215726
+GENE_0001809	9.01718343716873	10.5278463832732	12.4581527212512	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	11.1135190464703	10.3516241433696	10.4913915077668	10.7784388104248	10.9734992497901	9.39047195397465	10.9259440201303	9.08921822591037	8.9259440201303
+GENE_0001844	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0002231	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0002319	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0002401	9.01718343716873	8.94288388255201	13.3512375173347	10.817826403275	12.0025215600635	11.7940650455742	9.74669322641589	9.52855654574918	8.76666164264849	10.4913915077668	11.515404404591	12.8479683677062	12.8499035726119	9.34098151940914	11.896573147968	8.9259440201303
+GENE_0002494	12.7176231553098	11.7502388046096	9.65079779919357	10.817826403275	10.780129138727	11.7940650455742	11.331655727137	11.8504846406365	11.5740165647061	8.90642900704567	11.515404404591	9.38853674906894	12.1978268760323	13.2478721150177	11.4111463207977	11.7332989421879
+GENE_0002571	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0003914	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0003940	18.7936164696135	18.5259666500549	18.767141760431	18.7465914985063	18.4736160962264	18.452276528326	18.3577180237232	18.4264020017547	19.1340763938953	19.0214726572074	18.9332569194769	18.680858381871	18.8478528330472	18.8704120735553	18.6685341634904	19.0870759031146
+GENE_0004029	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0004039	15.6753949199205	15.9981663180532	16.0937412950423	15.7085973335202	15.0280566521706	16.3176270016313	14.6046742215435	16.0677153568572	14.7439415661484	15.3493725028944	15.9077218273698	15.7979276852066	15.4989964107528	14.8955703710868	15.238965345415	16.2388269754146
+GENE_0004049	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	10.9259440201303	9.08921822591037	8.9259440201303
+GENE_0004059	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	11.1135190464703	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
+GENE_0004069	10.6021459378899	10.5278463832732	11.2357602999147	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	11.6629096142965	10.6741807266315	8.9259440201303
+GENE_0004079	13.5407453932257	13.466445838609	13.7382606404439	13.3203267438042	14.2395607573643	13.5595997919372	13.2061248450532	14.0521185018062	13.521549144812	13.9508231264041	13.1003669053122	13.2954273446775	13.0909116721157	12.5109065208515	12.9961088215189	13.1738715335739
+GENE_0004089	17.4392482033415	17.575879079695	16.9636807544779	17.3256210434737	17.6172314041787	17.5435993132435	17.5604744176329	17.0123723230134	16.9113198854804	17.3452208596239	17.176469884398	16.95077917329	17.2546580986289	17.5841555028821	17.7294631621327	17.1880388655005
+GENE_0004099	18.1795747659256	18.3920325279274	18.3196827834598	18.333526241559	18.5148387589529	18.4292389922492	18.7382150724916	18.7009840543947	17.9834075008438	17.892270944049	18.0730595593165	18.5152412219121	18.2201946890607	18.0448850928538	18.2516095546673	17.6229115463646
+GENE_0004111	9.01718343716873	8.94288388255201	9.65079779919357	9.23286390255383	9.19516663800588	9.47213695068688	9.74669322641589	9.52855654574918	8.76666164264849	8.90642900704567	9.19347630970368	9.38853674906894	9.39047195397465	9.34098151940914	9.08921822591037	8.9259440201303
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/voom_transform.R	Wed Jan 25 10:13:10 2017 -0500
@@ -0,0 +1,18 @@
+#!/usr/bin/env Rscript
+
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+library("getopt")
+library("limma")
+
+spec <- matrix(c( 
+    "expressionmatrix", "e", 1, "character",
+    "transformedmatrix", "t", 1, "character"
+    ), byrow=TRUE, ncol=4)
+opt <- getopt(spec)
+
+em <-  read.delim(opt$expressionmatrix,header=T,row.names=1,stringsAsFactors=F,check.names=FALSE,na.strings=c(""))
+
+vem <- voom(em)
+write.table(file=opt$transformedmatrix,vem$E,sep="\t",row.names=TRUE,col.names=NA,quote=F)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/voom_transform.xml	Wed Jan 25 10:13:10 2017 -0500
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="voom_transform" name="Voom transform" version="3.29.0-0">
+    <description>transform count data to fit linear modelling</description>
+    <requirements>
+        <requirement type="package" version="3.29.0">bioconductor-limma</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+    </requirements>
+    
+    <version_command>echo $(R --version | grep -i version | head -n 1)", Limma: "$(R --vanilla --slave -e "library(limma) ; cat(sessionInfo()\$otherPkgs\$limma\$Version)")</version_command>
+    
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript
+            #if str($include_rdata) == 'true'
+                --save
+            #end if
+            '${__tool_directory__}/voom_transform.R'
+            -e '${input_select.expression_matrix}'
+            -t '${output_matrix}'
+        
+        #if str($include_rdata) == 'true'
+            && cp '.RData' '$output_rdata'
+        #end if
+    
+    ]]></command>
+    
+    <inputs>
+        <conditional name="input_select">
+            <param name="input_format" type="select" label="Output format">
+                <option value="1">Single expression matrix (header + multi column)</option>
+                <!-- <option value="2">Count files (no header + 1 sample per file)</option>-->
+            </param>
+            
+            <when value="1">
+                <param name="expression_matrix" type="data" format="txt,tabular" />
+            </when>
+            <!-- 
+            <when value="2">
+                repeat / input type = multiple
+            </when>
+             -->
+        </conditional>
+        
+        <param name="include_rdata" type="boolean" truevalue="true" falsevalue="" label="Save RData object" />
+        
+        <!-- normalization param
+        -->
+        
+    </inputs>
+    
+    <outputs>
+        <data name="output_matrix" format="tabular"
+              label="${tool.name} on $on_string" />
+
+        <data name="output_rdata" format="RData" label="${tool.name} on $on_string (RData)">
+            <filter>str(include_rdata) in ['true', true]</filter>
+        </data>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_format" value="1" />
+            <param name="expression_matrix" value="em.txt" />
+             
+            <output name="output_matrix" value="em_transformed.txt" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+        
+    ]]></help>
+    
+    <citations>
+        <citation type="doi">10.1093/nar/gkv007</citation>
+    </citations>
+</tool>