Mercurial > repos > melpetera > intensity_checks

changeset 6:ec75de7f1e08 draft default tip

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Uploaded
author melpetera
date Mon, 11 Dec 2023 12:56:20 +0000
parents a31f3f802b2b
children
files Intchecks/README.md Intchecks/Script_intensity_check.R Intchecks/parseargs.R Intchecks/test-data/input_IC_DM.txt Intchecks/test-data/input_IC_SM.txt Intchecks/test-data/input_IC_VM.txt Intchecks/test-data/output_IC_VM.tabular Intchecks/wrapper_intensity_check.R Intchecks/xml_intensity_check.xml
diffstat 9 files changed, 160 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/Intchecks/README.md	Wed Jan 22 09:34:08 2020 -0500
+++ b/Intchecks/README.md	Mon Dec 11 12:56:20 2023 +0000
@@ -5,7 +5,7 @@
 -----------
 
  * **@name**: Intensity check
- * **@version**: 1.2.8
+ * **@version**: 1.3.0
  * **@authors**: Original code: Anthony Fernandes (PFEM - INRA) - Maintainer: Melanie Petera (PFEM - INRAE - MetaboHUB)
  * **@init date**: 2018, September
  * **@main usage**: This tool computes some statistical measures, number of missing values and mean fold change.
@@ -25,8 +25,8 @@
 -----------
 
 ### Requirement:
- * R software: version > 3.0.0 recommended
- * Specific R libraries: 'batch' 
+ * R software: version > 4.0.0 recommended
+ * Specific R libraries: none 
 
 
 Technical description
--- a/Intchecks/Script_intensity_check.R	Wed Jan 22 09:34:08 2020 -0500
+++ b/Intchecks/Script_intensity_check.R	Mon Dec 11 12:56:20 2023 +0000
@@ -20,7 +20,7 @@
   VM.name <- "vM_NA.tabular"
   method <- "one_class"
   chosen.stat <- "mean,sd,quartile,decile,NA" 
-  class.col <- "2" 
+  class.col <- "uv" 
   test.fold <- "Yes" 
   class1 <- "Pools"
   fold.frac <- "Top"
@@ -97,11 +97,9 @@
 
 
   if(method != "no_class"){
-    
-    class.col <- colnames(SM)[as.numeric(class.col)]
   
     if(!(class.col %in% colnames(SM))){
-      stop("\n- - - - - - - - -\n", "The column ",class.col, " is not a part of the specify sample Metadata","\n- - - - - - - - -\n")
+      stop("\n- - - - - - - - -\n", "The ",class.col, " column is not found in the specified sample metadata file.","\n- - - - - - - - -\n")
     }
   
     c_class <- SM[,class.col]
@@ -110,7 +108,7 @@
     classnames <- levels(c_class)
   
     if((nb_class < 2)&&(test.fold=="Yes")){
-      err.1class <- c("\n The column",class.col, "contains only one class, fold calculation could not be executed. \n")
+      err.1class <- c("\n The ",class.col, " column contains only one class, fold calculation could not be executed. \n")
       cat(err.1class)  
     }
   
@@ -125,7 +123,7 @@
       if(!(class1 %in% classnames)){
         list.class1 <- c("\n Classes:",classnames,"\n")
         cat(list.class1)
-        err.class1 <- c("The class ",class1, " does not appear in the column ", class.col)
+        err.class1 <- c("The ",class1, " class does not appear in the ",class.col," column.")
         stop("\n- - - - - - - - -\n", err.class1,"\n- - - - - - - - -\n")
       }
   
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Intchecks/parseargs.R	Mon Dec 11 12:56:20 2023 +0000
@@ -0,0 +1,53 @@
+# parseCommandArgs function
+parse_args <- function(
+  args = NULL,
+  convert_booleans = TRUE,
+  convert_numerics = TRUE
+) {
+  if (is.null(args)) {
+    args <- commandArgs()
+  }
+  start <- which(args == "--args")[1] + 1
+  if (is.na(start)) {
+    return(list())
+  }
+  seq_by2 <- seq(start, length(args), by = 2)
+  result <- as.list(args[seq_by2 + 1])
+  names(result) <- args[seq_by2]
+  converters <- c()
+  if (convert_booleans) {
+    converters <- c(
+      converters,
+      function(x) {
+        return(if (x == "TRUE") TRUE else if (x == "FALSE") FALSE else x)
+      }
+    )
+  }
+  if (convert_numerics) {
+    converters <- c(
+      converters,
+      function(x) {
+        return(if (is.na(y <- as.numeric(x))) x else y)
+      }
+    )
+  }
+  return(convert_parameters(result, converters))
+}
+
+convert_parameters <- function(args, converters) {
+  suppressWarnings(
+    for (param in names(args)) {
+      for (converter in converters) {
+        old_value <- args[[param]]
+        args[[param]] <- converter(args[[param]])
+        if (!identical(args[[param]], old_value)) {
+          ## The value has been modified by the converter, and
+          ## we don't want values to be converted multiple times,
+          ## so we pass to the next value.
+          break
+        }
+      }
+    }
+  )
+  return(args)
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Intchecks/test-data/input_IC_DM.txt	Mon Dec 11 12:56:20 2023 +0000
@@ -0,0 +1,18 @@
+data	j 785	 y54j 68y4j6	5-6 4	hrh 	5h -	3	 t564	t54 66	 y6y	t6 5h	(5y 	 g51 	(	6	 98 j7-0 	06654h 	60
+5d_-kkcùf	0.356426723610756	0.380152310071702	0.0306944207412024	0.334137638848017	0.298147485608469	0.975073793297568	0.129099504745855	0.973451663994064	0.334792719284834	0.0751565260418877	0.322897933010729	0.129033714279026	0.722966330196726	0.580654367692078	0.644502528016206	0.352827235332827	0.511778286438001
+npèt	0.801750949101246	0.535593104115636	0.258351312473067	0.599475573145688	0.0763319665667417	0.504558103160623	0.367963830290116	0.440540211857668	0.158066366765388	0.609574253877002	0.550590276177951	0.232864384033621	0.637065775537391	0.424098276140436	0.662053737304139	0.0217541227637467	0.299053946391647
+5PY4(*3	0.875199970420953	NA	0.253659010703906	0.507762246807195	0.856444177031262	NA	0.616538655402613	0.388475672176377	0.914254939740854	0.449607330807756	0.628469388494906	0.436558212905713	0.951198610265672	0.956459387015831	0.0113483457928278	0.611559621193868	0.127393349941781
+k	0.235214515530521	0.50917637648828	0.0303152651414629	0.305595242012361	0.470145996588881	0.356776179776951	0.569840649303474	0.720070419680388	0.875026990189028	0.97246313990283	0.936423978578332	0.810603455355391	0.903046784946495	0.667091730522105	0.0282601148338295	0.276666638740528	0.747503427028951
+"t v^ptok!R/; "	0.251801918471682	0.871383805557867	0.285183681272061	0.552739436194454	0.863766301215097	0.182656918760194	0.977603710051043	0.204845724382198	0.751690583305025	0.751475804910098	0.938399878874186	0.218163132174348	0.523463794277572	0.987156468237196	0.630938391969655	0.495061607430081	0.815474132321848
+ojt*	0.907412839750932	0.857498273276021	0.370137361785406	0.76678484779183	0.213299689296413	0.521214352529346	0.0851731095099456	0.868227767553325	0.0711706993343434	NA	0.700568035764899	NA	0.570332959002042	0.23270290523468	NA	NA	0.466363859676536
+lmtki	0.344288940919619	0.308219131305663	0.218449898667526	0.700869668247368	0.932538878977527	0.396198994630489	0.710306820874376	0.124235068279782	0.56608643523601	0.887647287670482	0.0375011938139768	0.282378766400105	0.757492159558571	0.506567258021703	0.990910788272054	0.326205008250378	0.61003856679129
+1h6-(587 t	0.308709890328272	0.717202505490233	0.777934118812417	NA	0.588458968776734	0.940112596977594	0.788662314418432	0.133046934771924	0.891405172730758	0.915119678712577	0.401136527896346	0.996068607925829	0.049077648050296	0.157657286859101	0.598183619914656	0.439531332356748	0.11995300831499
+r154 (54 86	0.0861033910635205	0.243889357950567	0.848801588667359	0.972183114768299	0.311829870889657	0.434854970574638	0.0240613698880671	0.273335646139236	0.902686361056168	0.73479376111027	0.232132726965829	0.471097756642369	0.511949019774828	0.934158039531663	0.60125450357768	0.972297241140637	0.63149263296722
+(h4 	0.336373953934809	0.521412085356266	0.281632887739949	0.67004516763179	0.0199332367594847	0.867732114278491	0.973477443505332	0.883197938525362	0.334509105447652	0.793947578560618	0.465167375556954	0.508757674191867	0.983758014396725	0.100582744588671	0.501301982240787	0.789637338939369	0.967382850752139
+2	0.65083934802851	NA	0.0376667088550816	0.514003854683931	0.274761574286474	0.652108809243866	0.689393057486628	0.262205073769319	0.871958663956254	0.709490850507154	0.854477673591409	0.672918329289054	0.141693817710263	0.00543057257281332	0.273084303937691	0.39570748778882	0.303196826092465
+ m(yk	0.798331012769621	0.806128809071498	0.519974578571807	0.0237856823099186	0.396426673475168	0.75979784245693	0.0589336105092753	0.763144123705766	0.16086904822931	0.301000258395631	0.321186481311644	0.0091434029302796	0.0346149352313591	0.276366137673702	NA	NA	NA
+ -546 -3 -3	0.981561422839383	0.755973696318293	0.328878596436459	0.233341270249666	0.14569201922932	0.458105216271765	NA	0.775603857680909	0.146769440956804	0.86812372109824	0.601678275863019	0.782019307745586	0.955614654474782	0.836058192741214	0.454550085076576	0.181788519803465	0.325277631599655
+nz^à  t 	0.920089977342539	NA	0.105577675363886	0.805216649434891	0.505774902707566	0.619612431793644	0.337662179244335	0.672829320507873	0.387228581340173	0.209795853201976	0.0403285073621635	0.540614252108851	0.43362855410287	0.160204078494507	0.924783730297701	0.116837628312753	0.58763473928668
+kzjù	0.418651623550921	0.668434005412235	0.845525871017258	0.567468950919516	0.111441846749533	0.411424602517146	0.0743349602270699	0.583730221710347	0.0105008018078939	0.918789674284249	0.808643595994088	0.33578972219198	0.536848200622412	0.898842910125025	0.333954421105444	0.0390509357521919	0.159857705429294
+. Glk(ôepjg$	0.3266193089274	0.806668730531573	0.87265879590923	0.934940869880726	0.548967615908753	0.250539517744596	0.75436043048449	0.597444122305604	0.343955002787363	0.560987092777944	0.134929631392942	0.958047956861493	0.870429681664852	0.66286672214456	0.441523248613101	0.437073092741238	0.265031623006715
+rmlgj*lr ,	0.462672931523031	0.74679446664976	0.151929368261195	0.165870989887449	0.90931621240424	0.423706631494886	0.337742032589001	0.184993498717115	0.0792523932129463	0.071353352835237	0.525247607449536	0.647744088759121	0.158725526449032	0.203927461340644	0.20055683200405	0.897053444943847	0.506954538974894
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Intchecks/test-data/input_IC_SM.txt	Mon Dec 11 12:56:20 2023 +0000
@@ -0,0 +1,18 @@
+data	ABCD	E	AAA	fp	uv
+j 785	1	91	a	a	s
+y54j 68y4j6	2	60	b	z	d
+5-6 4	2	43	c	e	f
+hrh	3	24	d	r	s
+5h -	4	29	b	t	d
+3	56	71	a	y	f
+t564	4	4	r	u	s
+t54 66	23	91	c	i	d
+y6y	5	61	f	o	f
+t6 5h	8	21	s	p	s
+(5y	98	77	b	q	d
+g51	67	1	b	s	f
+(	98	48	r	d	s
+6	2	10	a	f	d
+98 j7-0	1	36	a	g	f
+06654h	34	100	k	h	s
+60	67	38	d	j	d
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Intchecks/test-data/input_IC_VM.txt	Mon Dec 11 12:56:20 2023 +0000
@@ -0,0 +1,18 @@
+variable	A	B	C	D
+5d_-kkcùf	0	a	ze$ùj	0
+npèt	1	b	 g	0
+5PY4(*3	2	c	 15j-è,	0
+k	3	a	6jè	1
+t v^ptok!R/; 	4	b	8j4,	1
+ojt*	5	c	5èj1	1
+lmtki	6	a	j84	2
+1h6-(587 t	7	b	j4e54	2
+r154 (54 86	8	c	j	2
+(h4 	9	a	54j6@44èu6(è4	3
+2	10	b	(51h	3
+ m(yk	11	c	8-1	3
+ -546 -3 -3	12	a	hy-81u	4
+nz^à  t 	13	b	zs5-hj1	4
+kzjù	14	c	861h	4
+. Glk(ôepjg$	15	a	(8168(h1	9
+rmlgj*lr ,	16	b	8hjè1	9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Intchecks/test-data/output_IC_VM.tabular	Mon Dec 11 12:56:20 2023 +0000
@@ -0,0 +1,18 @@
+variable	A	B	C	D	Mean_s	Mean_Other	Sd_s	Sd_Other	NA_s	NA_Other	Pct_NA_s	Pct_NA_Other	log2_fold_Other_VS_s
+5d_-kkcùf	0	a	ze$ùj	0	0.328435659796011	0.471016292948534	0.228451584966275	0.306556034161105	0	0	0	0	0.520166189269251
+npèt	1	b	 g	0	0.506264084119198	0.376554698635174	0.274830786331717	0.183936635993605	0	0	0	0	-0.427030691648967
+5PY4(*3	2	c	 15j-è,	0	0.668644405816343	0.50811805375594	0.201164644457448	0.349587008290475	0	2	0	18.1818	-0.396075445063365
+k	3	a	6jè	1	0.543804495072701	0.559217630380327	0.327662996370251	0.314841391119243	0	0	0	0	0.040321768397534
+t v^ptok!R/; 	4	b	8j4,	1	0.592024378555822	0.613605365279061	0.247181366605864	0.324224837252577	0	0	0	0	0.0516545128160351
+ojt*	5	c	5èj1	1	0.582425939013687	0.477909216050108	0.359170947930419	0.286185546056577	2	2	33.3333	18.1818	-0.285338020130744
+lmtki	6	a	j84	2	0.621134980920132	0.452102270945102	0.231326066781317	0.308002376571479	0	0	0	0	-0.458257654955689
+1h6-(587 t	7	b	j4e54	2	0.500220172773265	0.574650849860962	0.353280826805041	0.328577697095778	1	0	16.6667	0	0.200122420718524
+r154 (54 86	8	c	j	2	0.550231316290937	0.535048495905671	0.420471482717973	0.267498028870002	0	0	0	0	-0.0403685917338988
+(h4 	9	a	54j6@44èu6(è4	3	0.757873249494774	0.495600908676148	0.238828322527637	0.310985735881046	0	0	0	0	-0.612777752412226
+2	10	b	(51h	3	0.516854736034218	0.420780853559443	0.219207900924983	0.318004326311928	0	1	0	9.0909	-0.296689802273714
+ m(yk	11	c	8-1	3	0.243333099843161	0.445893010825123	0.330573629082567	0.285737925809767	1	2	16.6667	18.1818	0.873765007290379
+ -546 -3 -3	12	a	hy-81u	4	0.644085917693107	0.510055119992691	0.40111184763981	0.256342273516465	1	0	16.6667	0	-0.336599986295532
+nz^à  t 	13	b	zs5-hj1	4	0.470538473606561	0.454458821926304	0.3244119263237	0.280532541853305	0	1	0	9.0909	-0.0501631106824151
+kzjù	14	c	861h	4	0.425857390892727	0.46983142764184	0.331238344963174	0.311088298141582	0	0	0	0	0.141772831906062
+. Glk(ôepjg$	15	a	(8168(h1	9	0.647401746079442	0.534784815200539	0.244322481422829	0.27318926988152	0	0	0	0	-0.275702754775479
+rmlgj*lr ,	16	b	8hjè1	9	0.348903046371266	0.41640209993349	0.303393826442722	0.274707725036023	0	0	0	0	0.255151150062007
--- a/Intchecks/wrapper_intensity_check.R	Wed Jan 22 09:34:08 2020 -0500
+++ b/Intchecks/wrapper_intensity_check.R	Mon Dec 11 12:56:20 2023 +0000
@@ -14,17 +14,15 @@
 #                                                                           #
 #############################################################################
 
-
-library(batch) #necessary for parseCommandArgs function
-args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
-
 source_local <- function(...){
   argv <- commandArgs(trailingOnly = FALSE)
   base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
   for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
 }
 #Import the different functions
-source_local("Script_intensity_check.R", "RcheckLibrary.R")
+source_local("parseargs.R", "Script_intensity_check.R", "RcheckLibrary.R")
+
+args = parse_args() #interpretation of arguments given in command line as an R list of objects
 
 
 if(length(args) < 7){ stop("NOT enough argument !!!") }
--- a/Intchecks/xml_intensity_check.xml	Wed Jan 22 09:34:08 2020 -0500
+++ b/Intchecks/xml_intensity_check.xml	Mon Dec 11 12:56:20 2023 +0000
@@ -1,7 +1,7 @@
-<tool id="intens_check" name="Intensity Check" version="1.2.8">
+<tool id="intens_check" name="Intensity Check" version="1.3.0">
 	<description>Statistical measures, number of missing values and mean fold change</description>
 	<requirements>
-	    <requirement type="package" version="1.1_5">r-batch</requirement>
+	    <requirement type="package" version="4.2.1">r-base</requirement>
 	</requirements>
 	<command interpreter="Rscript">
   
@@ -66,7 +66,7 @@
 			</when>
 			
 			<when value="each_class">
-				<param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
+				<param name="class_col" type="text" label="Class column" help="Name of the column in Sample metadata" />
 				<param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
 					<option value="mean">Mean</option>
                     <option value="sd">Standard deviation</option>
@@ -87,11 +87,13 @@
 							<option value="log10">log10 </option>
 						</param>
 					</when>
+					<when value="No">
+					</when>
 				</conditional>
 			</when>
 			
 			<when value="one_class">
-				<param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
+				<param name="class_col" type="text" label="Class column" help="Name of the column in Sample metadata" />
 				<param name="class1" type="text" label="Selected class" help="Name of the class to test versus all the remaining samples." />
 				<param name="chosen_stat" type="select" display="checkboxes" multiple="True" label="Statistics">
 					<option value="mean">Mean</option>
@@ -117,6 +119,8 @@
 							<option value="log10">log10 </option>
 						</param>
 					</when>
+					<when value="No">
+					</when>
 				</conditional>
 			</when>
 		</conditional>
@@ -129,7 +133,21 @@
 	</outputs>
 	
 	
-
+  <tests>
+	<test>
+      <param name="dataMatrix_in" value="input_IC_DM.txt"/>
+      <param name="sampleMetadata_in" value="input_IC_SM.txt"/>
+      <param name="variableMetadata_in" value="input_IC_VM.txt"/>
+	  <param name="method" value="one_class"/>
+	  <param name="chosen_stat" value="mean,sd,NA"/>
+	  <param name="class_col" value="uv"/>
+	  <param name="class1" value="s"/>
+	  <param name="test_fold" value="Yes"/>
+	  <param name="fold_frac" value="Bottom"/>
+	  <param name="logarithm" value="log2"/>
+      <output name="variableMetadata_out" file="output_IC_VM.tabular"/>
+	</test>
+  </tests>
 	
 	<help>
 
@@ -194,7 +212,7 @@
 	|  Select the statistical measures you want to add in the variable metadata table. If the method is "each class" or "one class", you can choose to leave this section blank if you only want to calculate the mean fold change (see below).
 
 **Class column** (*only if "each class" or "one class"*)
-	| Select the class column in sample metadata table.
+	| Fill the name of the class column in sample metadata table; it is case-sensitive.
 
 **Selected class** (*only if "one class"*)
 	| If the method is "one class", specify it. Remaining samples will be named "Other".
@@ -231,7 +249,7 @@
 .. class:: warningmark
 
 For more information about input files, refer to the corresponding "W4M HowTo" page:
- | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
+ | `W4M table format for Galaxy &lt;https://workflow4metabolomics.org/sites/default/files/fichiers/documents/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
  |