changeset 0:bcbd7179d8ec draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
author artbio
date Thu, 11 Jul 2019 13:31:20 -0400
parents
children a96cc346819c
files center_scale.R center_scale.xml test-data/full_center.tab test-data/full_standardize.tab test-data/group_center.tab test-data/group_standardize.tab test-data/mini.data.counts.tsv test-data/mini.data.factor.tsv
diffstat 8 files changed, 427 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/center_scale.R	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,101 @@
+options( show.error.messages=F,
+       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+warnings()
+library(optparse)
+
+# Arguments
+option_list = list(
+  make_option(
+    '--data',
+    default = NA,
+    type = 'character',
+    help = "Input file that contains values to transform. Must be tabular separated,
+            with columns and row names, variables in rows, observations in columns  [default : '%default' ]"
+  ),
+  make_option(
+   '--center',
+    default = TRUE,
+    type = 'logical',
+    help = "center data to the mean [default : '%default' ]"
+  ),
+  make_option(
+   '--scale',
+    default = TRUE,
+    type = 'logical',
+    help = "scale data to standard deviation [default : '%default' ]"
+  ),
+  make_option(
+    '--factor',
+    default = '',
+    type = 'character',
+    help = "A two-column observations|factor_levels table, to group observations to be transformed by levels  [default : '%default' ]"
+  ),
+  make_option(
+    '--output',
+    default = 'res.tab',
+    type = 'character',
+    help = "Table of transformed values [default : '%default' ]"
+  )
+)
+
+transform <- function(df, center=TRUE, scale=TRUE) {
+    transfo <- scale(
+        t(df),
+        center=center,
+        scale=center
+        )
+    return(as.data.frame(t(transfo)))
+}
+
+opt = parse_args(OptionParser(option_list = option_list),
+                 args = commandArgs(trailingOnly = TRUE))
+
+data = read.table(
+    opt$data,
+    check.names = FALSE,
+    header = TRUE,
+    row.names = 1,
+    sep = '\t'
+)
+
+if (opt$factor != '') {
+    data.factor = read.table(
+        opt$factor,
+        check.names = FALSE,
+        header = TRUE,
+        sep = '\t'
+        )
+    colnames(data.factor) <- c("cellid", "level")
+    data.transformed <- data.frame(row.names=rownames(data), stringsAsFactors=FALSE)
+    for (group in levels(data.factor$level)){
+        subcells <- as.data.frame(subset(data.factor, level==group, select=cellid))
+        subdata <- as.data.frame(subset(data, select=subcells$cellid))
+        subdata.transformed <- transform(subdata, center=opt$center, scale=opt$scale)
+        data.transformed <- cbind(data.transformed, subdata.transformed)
+    }
+} else {
+    data.transformed <- transform(data, center=opt$center, scale=opt$scale)
+}
+
+
+write.table(
+  cbind(gene=rownames(data.transformed), data.transformed),
+  opt$output,
+  col.names = TRUE,
+  row.names = FALSE,
+  quote = F,
+  sep = "\t"
+)
+
+
+
+
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/center_scale.xml	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,105 @@
+<tool id="center_scale" name="Center or scale (standardize) data" version="0.9.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="1.6.0">r-optparse</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[ 
+        Rscript $__tool_directory__/center_scale.R 
+            --data '$input'
+            --center '$center'
+            --scale '$scale'
+            #if $factor.factor_options == 'TRUE':
+               --factor '$file'
+            #end if
+            --output '$output'
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Input file with values to transform"
+               help="Must be tabular separated with columns and row names, variables in rows, observations in columns" />
+        <param name="center" type="select" label="Center data to mean">
+            <option value="TRUE" selected="true">Yes</option>
+            <option value="FALSE">No</option>
+        </param>
+        <param name="scale" type="select" label="Scale data to standard deviation">
+            <option value="TRUE" selected="true">Yes</option>
+            <option value="FALSE">No</option>
+        </param>
+        <conditional name="factor">
+            <param name="factor_options" type="select" label="group data by factor ?">
+                <option value="TRUE">Yes</option>
+                <option value="FALSE" selected="true">No</option>
+            </param>
+            <when value="TRUE">
+                <param name="file" type="data" format="tabular" label="Grouping map"
+                       help="A two-column observation|factor_level table that assigns group ids to observations" /> 
+            </when>
+            <when value="FALSE">
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="scale ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="mini.data.counts.tsv" ftype="tabular"/>
+            <output name="output" file="full_standardize.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="mini.data.counts.tsv" ftype="tabular"/>
+            <param name="scale" value="FALSE"/>
+            <output name="output" file="full_center.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="mini.data.counts.tsv" ftype="tabular" />
+            <param name="factor_options" value="TRUE" />
+            <param name="file" value="mini.data.factor.tsv" ftype="tabular" />          
+            <output name="output" file="group_standardize.tab" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="input" value="mini.data.counts.tsv" ftype="tabular" />
+            <param name="scale" value="FALSE"/>
+            <param name="factor_options" value="TRUE" />
+            <param name="file" value="mini.data.factor.tsv" ftype="tabular" />          
+            <output name="output" file="group_center.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+The tool perform various normalization operations on a data table, including mean centering,
+standard deviation rescaling, or both (standardization).
+
+In addition, these operations can be performed on subsets of observations, is the user provides
+a two-column table that maps observations to groups (factor levels).
+
+**Inputs**
+
+A data table with observations (samples, library sequencings) in columns (library names
+are column names) and variables (genes) in rows (gene names are row names).
+
+Optionally, a two-column table may be used to map observations to a factor level. In this
+case, normalization operations will be performed by group having same level.
+
+**Outputs**
+
+A table with same numbers of columns and rows as input table, and transformed values.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+        @Manual{,
+             title = {R: A Language and Environment for Statistical Computing},
+             author = {{R Core Team}},
+             organization = {R Foundation for Statistical Computing},
+             address = {Vienna, Austria},
+             year = {2014},
+             url = {http://www.R-project.org/},
+        }
+        </citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/full_center.tab	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,24 @@
+gene	V1	V2	V3	V4	V5	V6	V7	V8	V9	V10	V11	V12	V13	V14	V15	V16	V17	V18	V19	V20	V21	V22	V23	V24	V25	V26	V27	V28	V29	V30	V31	V32	V33	V34	V35	V36	V37	V38	V39	V40	V41	V42	V43	V44	V45	V46	V47	V48	V49	V50	V51	V52	V53	V54	V55	V56	V57	V58	V59	V60	V61	V62	V63	V64	V65	V66	V67	V68	V69	V70	V71	V72	V73	V74	V75	V76	V77	V78	V79	V80	V81	V82	V83	V84	V85	V86	V87	V88	V89	V90	V91	V92	V93	V94	V95	V96	V97	V98	V99	V100
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+var_2	-0.541294731712273	0.242227703329583	0.298457497163882	-1.59128040481661	0.492568820762451	-1.39513076577133	0.326846703851359	-0.00765721677150041	1.36292463524707	-1.16295544550248	-1.48399920753179	0.992534842020315	0.65782034548078	0.914972097464969	0.674982769172224	0.906021959186926	-0.430941433135481	0.579077508030049	-0.723551394152942	1.0640090777793	1.00766589564849	-1.2217881910531	1.26363116354427	0.752596538382718	1.5479746302466	0.284040522571208	1.4250198057911	-1.15253249925345	1.6598395481262	-0.948344426203957	0.884033459138658	1.41476147992376	-0.347957924430969	-1.64559941588015	1.06132163629135	-1.5878917833097	-1.29702873221215	0.16007281182391	1.35686994772062	1.26935792924921	-0.215505740939617	1.57086144476489	1.44430164224152	1.24316088063912	1.48515104059891	1.64290468769636	0.618432445070096	-0.371375964112492	-0.034557822626917	-0.29952346835281	-1.34816900807847	-1.61764908416048	-1.45111420161824	-0.812096005551296	-0.997930629277508	0.269326020526353	0.14020729154829	1.31489076490235	-0.314589723189421	-0.689536732933039	-1.04476819352643	1.09271152807006	-0.788621641964541	-0.0359206339779884	-1.37766073744226	-0.893794745124963	-1.59495927885248	-0.735358451294217	0.122548288987079	-0.272600295676175	0.228717881291509	0.272130161363657	1.43964717470135	0.120524068606268	-0.521467807510908	-0.573733985374251	0.62940506053399	-1.0972800288116	1.05936837733075	-1.05847160961555	1.62005588218622	-0.187743541207902	-0.529256421403206	1.41482790762811	-0.91322796400769	-0.481318233441152	1.12599404818718	-0.458520040074382	-0.326683777382395	0.063673926711384	0.33634397052215	-0.391935123347221	-0.347679969762858	-1.66415455450474	-1.4105070877922	-1.57122334443858	0.0207060807317143	0.790029465599748	-0.709276246121835	0.010616296847664
+var_3	0.828679126763805	-1.31436590033886	-0.936059531319347	-0.756825170473032	-0.878038176234384	0.129721330372601	0.567286029053015	-0.149033923252748	0.0164349136912808	0.636331490569958	2.25513195953757	0.745117105537781	-2.09575578911293	-0.467442155317868	-0.731554403243438	-0.688780168352447	2.61744500839296	1.0076224407424	-0.955460087535743	-0.385928532728328	-0.456410748799656	1.81753220261037	1.58108096237827	-1.31982919111739	-1.25200853654515	1.70530961837567	0.78124521454655	-0.918332286658345	0.172110142759496	-0.432473890953326	-0.180824734926549	-1.24900167993743	-0.104643688293381	0.448101077918828	0.0258454734114866	0.883981512253873	-0.260671364395439	0.443657123316603	0.694599978531318	0.150752995809882	-0.879236057761994	1.51156661300589	-0.420671435574607	1.82603036294378	-0.088723076515399	-0.151915620976093	-1.13437375688035	0.56110096649141	-0.383513636485153	0.183499944322951	0.413910404978128	0.95999065708525	0.148828580741724	-1.36457642822887	0.734525796207191	-1.33442489767532	0.585605698774797	0.613936494746417	-0.419331935204972	0.0666188646250627	-0.932206093063733	0.0647799677261241	0.48947202085126	3.15416455186692	-0.871111586405689	-1.14470374278961	-1.25831186570738	1.45048709629642	0.123456728128873	-0.45951669999386	-1.27439867456517	1.00839101361375	0.965105491160971	-0.100733702633268	-0.114029848360004	0.872578248439622	-2.44573717649276	1.07579564179439	-1.22008819885551	-0.549462113787089	-1.36154999740461	0.2411130367276	0.6657518611908	-0.80642238631606	-0.330703275441858	-0.964909549003239	-0.876496108507171	0.596684655690397	0.528215082290121	0.420773930698013	-0.506073429427802	0.364004117157493	0.139413668560793	-0.470387168679385	-0.430967829944663	-0.225649722628602	0.747186684974797	-1.40629731082984	1.48766254740408	-0.0486731493928695
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/full_standardize.tab	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,24 @@
+gene	V1	V2	V3	V4	V5	V6	V7	V8	V9	V10	V11	V12	V13	V14	V15	V16	V17	V18	V19	V20	V21	V22	V23	V24	V25	V26	V27	V28	V29	V30	V31	V32	V33	V34	V35	V36	V37	V38	V39	V40	V41	V42	V43	V44	V45	V46	V47	V48	V49	V50	V51	V52	V53	V54	V55	V56	V57	V58	V59	V60	V61	V62	V63	V64	V65	V66	V67	V68	V69	V70	V71	V72	V73	V74	V75	V76	V77	V78	V79	V80	V81	V82	V83	V84	V85	V86	V87	V88	V89	V90	V91	V92	V93	V94	V95	V96	V97	V98	V99	V100
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+var_3	0.828679126763805	-1.31436590033886	-0.936059531319347	-0.756825170473032	-0.878038176234384	0.129721330372601	0.567286029053015	-0.149033923252748	0.0164349136912808	0.636331490569958	2.25513195953757	0.745117105537781	-2.09575578911293	-0.467442155317868	-0.731554403243438	-0.688780168352447	2.61744500839296	1.0076224407424	-0.955460087535743	-0.385928532728328	-0.456410748799656	1.81753220261037	1.58108096237827	-1.31982919111739	-1.25200853654515	1.70530961837567	0.78124521454655	-0.918332286658345	0.172110142759496	-0.432473890953326	-0.180824734926549	-1.24900167993743	-0.104643688293381	0.448101077918828	0.0258454734114866	0.883981512253873	-0.260671364395439	0.443657123316603	0.694599978531318	0.150752995809882	-0.879236057761994	1.51156661300589	-0.420671435574607	1.82603036294378	-0.088723076515399	-0.151915620976093	-1.13437375688035	0.56110096649141	-0.383513636485153	0.183499944322951	0.413910404978128	0.95999065708525	0.148828580741724	-1.36457642822887	0.734525796207191	-1.33442489767532	0.585605698774797	0.613936494746417	-0.419331935204972	0.0666188646250627	-0.932206093063733	0.0647799677261241	0.48947202085126	3.15416455186692	-0.871111586405689	-1.14470374278961	-1.25831186570738	1.45048709629642	0.123456728128873	-0.45951669999386	-1.27439867456517	1.00839101361375	0.965105491160971	-0.100733702633268	-0.114029848360004	0.872578248439622	-2.44573717649276	1.07579564179439	-1.22008819885551	-0.549462113787089	-1.36154999740461	0.2411130367276	0.6657518611908	-0.80642238631606	-0.330703275441858	-0.964909549003239	-0.876496108507171	0.596684655690397	0.528215082290121	0.420773930698013	-0.506073429427802	0.364004117157493	0.139413668560793	-0.470387168679385	-0.430967829944663	-0.225649722628602	0.747186684974797	-1.40629731082984	1.48766254740408	-0.0486731493928695
+var_4	0.570882716569773	-1.34996657693053	0.882426417475764	-0.354628538764074	0.123010066600641	-2.04905956489049	-0.765767467476612	-1.46390766921689	0.322082355773827	0.232250358936151	-1.35356973128321	-0.44264837062556	-0.991460246418388	0.0423773985255568	0.125257491643957	-2.38674825420891	-2.37494032502422	0.0295997771599167	-0.387988114645446	0.347738943510966	1.30218797083728	0.778763762023523	-0.0285795845337616	0.452104014022311	-0.0519204586678151	0.0986247000919088	0.473753466565958	0.912964311617811	-1.01016153912967	-1.56928895530399	1.85434676537891	-0.921677356144738	1.89160144994239	0.722717074957377	-0.674372535315653	-0.718924427982797	0.332745790994934	2.18620834443533	0.63032169461092	-0.290649130863158	0.918239711202058	-0.241010267423069	-0.159265145041944	-0.724560239501209	-0.0937534052676546	1.24648293234835	0.855922342184137	-0.639975612379489	0.926871857754904	-0.70338959377306	-0.140253522232597	-0.634257349065764	1.97657450513486	1.2245279482502	-1.13577216133295	1.25417205836626	1.00188343740811	0.0164610299117465	0.487830104097486	0.783809056801044	0.639233832024887	0.263073784235967	-0.645408629871763	2.7103043457555	0.82423515246283	-0.744465752990466	-0.980987816785612	0.0830193188085329	0.16178247193395	-0.0438718653545216	-0.555231437729293	0.0266362772244007	-0.074041554051169	-1.0858785472466	0.307719275776737	-0.911039168065625	-0.124968691055027	-1.89010333125783	-0.547434603500344	-0.787294165148244	-0.35151736513404	-1.27402446865972	1.11293261341547	0.485089679103526	-0.830394097225205	0.311010390643514	-0.39036287062895	-0.625425500763337	1.01552170639303	-1.22499971401974	-0.38498550511866	1.22644786020278	-0.492563186943068	0.658944987278176	-0.570542653102809	1.33254858861935	-1.50442146282735	0.549660238748154	1.95422493129708	1.03133322186475
+var_5	-0.44255825069139	1.86243263832627	0.0184399271121413	0.479438104915673	-0.44255825069139	-0.44255825069139	-1.36455460629845	-0.44255825069139	0.0184399271121413	-0.44255825069139	0.0184399271121413	-0.903556428494921	-1.36455460629845	0.0184399271121413	0.940436282719204	-1.36455460629845	-0.44255825069139	-1.82555278410198	-0.903556428494921	0.0184399271121413	0.940436282719204	2.3234308161298	-1.36455460629845	0.0184399271121413	-0.903556428494921	-0.903556428494921	0.0184399271121413	-0.903556428494921	0.0184399271121413	-0.44255825069139	-1.36455460629845	-0.903556428494921	0.479438104915673	-0.44255825069139	1.86243263832627	0.0184399271121413	-0.44255825069139	0.479438104915673	0.940436282719204	0.479438104915673	0.479438104915673	-0.903556428494921	-1.36455460629845	0.0184399271121413	-0.44255825069139	0.0184399271121413	0.479438104915673	1.86243263832627	0.940436282719204	0.479438104915673	0.940436282719204	0.940436282719204	2.3234308161298	1.40143446052274	-1.36455460629845	0.0184399271121413	-1.36455460629845	-0.903556428494921	0.479438104915673	0.479438104915673	0.479438104915673	-0.44255825069139	-0.44255825069139	1.40143446052274	0.479438104915673	-0.44255825069139	-0.44255825069139	-0.903556428494921	0.0184399271121413	-0.903556428494921	1.40143446052274	0.479438104915673	0.940436282719204	-0.903556428494921	0.0184399271121413	-1.36455460629845	-1.82555278410198	0.940436282719204	-0.903556428494921	0.0184399271121413	1.40143446052274	1.40143446052274	0.0184399271121413	-0.903556428494921	1.86243263832627	0.0184399271121413	-1.36455460629845	-0.903556428494921	1.40143446052274	1.40143446052274	0.0184399271121413	-0.903556428494921	-0.903556428494921	2.3234308161298	1.40143446052274	0.479438104915673	-0.903556428494921	0.479438104915673	-0.44255825069139	-0.903556428494921
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group_center.tab	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,24 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group_standardize.tab	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,24 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mini.data.counts.tsv	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,24 @@
+gene	V1	V2	V3	V4	V5	V6	V7	V8	V9	V10	V11	V12	V13	V14	V15	V16	V17	V18	V19	V20	V21	V22	V23	V24	V25	V26	V27	V28	V29	V30	V31	V32	V33	V34	V35	V36	V37	V38	V39	V40	V41	V42	V43	V44	V45	V46	V47	V48	V49	V50	V51	V52	V53	V54	V55	V56	V57	V58	V59	V60	V61	V62	V63	V64	V65	V66	V67	V68	V69	V70	V71	V72	V73	V74	V75	V76	V77	V78	V79	V80	V81	V82	V83	V84	V85	V86	V87	V88	V89	V90	V91	V92	V93	V94	V95	V96	V97	V98	V99	V100
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+var_21	10041892.5004772	10043128.6716551	9963303.95084781	9986222.08282607	9767447.68764638	9855375.97055651	9904538.66692104	9991176.6684989	9908581.42647719	9940947.39785716	9948547.53279308	10060654.6051984	9922842.34328386	10146731.1919473	10166213.2714846	9894107.44606133	10040724.1515591	9981664.93020822	10111663.5906796	9866621.19047036	9923923.7156163	9917568.84235943	9851840.69470509	10096767.3100085	9941483.03677652	10018672.0162746	9831557.01843229	10188126.782705	9957899.64088408	10076381.7203181	10085417.3868784	9941576.79903592	9917343.681467	10198179.1979889	9943227.95800052	10016944.1164676	9939167.08023155	9906467.1648156	10128611.0771038	9969211.50059073	9814075.46563147	10303090.0178485	10017824.1446116	9790947.51275142	10003881.3528496	9991616.79470837	9821637.01800175	9957450.13894481	9952713.40598301	10083829.4088331	10039622.2573642	10067480.128153	10053380.9581869	9812014.41814719	9852826.2010602	10021647.1268942	10059138.2829339	9964400.12005378	10104057.7628946	10043933.735712	9842026.36132698	10075267.5139342	10055455.0205628	9967054.56865608	10068898.9732625	9994664.66215774	9870979.96627774	10065109.2330585	9924768.24257857	10015404.5907916	10068641.1687354	10012805.1918731	9940666.55444529	9844840.14761603	10050368.6627738	9937198.61426193	10095344.5657685	10034016.188981	10017109.023408	9979103.4739344	9823501.73691051	10105170.8692053	10003405.9235025	9731840.75222966	10067205.3993506	10053211.9153879	9811305.83031889	10002961.568576	10090104.5023654	9880981.47827369	9954979.33566264	10182510.8895708	9833200.60350312	9945784.35939082	10047277.8355979	9790078.91802557	9960122.99971608	10110877.5490572	9917765.69201284	9986056.58750544
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mini.data.factor.tsv	Thu Jul 11 13:31:20 2019 -0400
@@ -0,0 +1,101 @@
+cell.id	factor
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