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changeset 0:f50bb34c1a37 draft

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planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
author caleb-easterly
date Wed, 21 Feb 2018 16:29:34 -0500
parents
children 34c1ae5e99ac
files peca.R peca.xml test-data/group1.txt test-data/group2.txt test-data/out.tab test-data/test.tab
diffstat 6 files changed, 117 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peca.R	Wed Feb 21 16:29:34 2018 -0500
@@ -0,0 +1,46 @@
+#!/usr/bin/env Rscript
+
+library(PECA)
+
+# Set up R error handling to go to stderr
+options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
+
+# Avoid crashing Galaxy with an UTF8 error on German LC settings
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+main <- function() {
+    args <- commandArgs(trailingOnly = TRUE)
+        
+    # read first argument, which is quant file (proteins in rows, samples in columns)
+    quant_file <- read.delim(args[1],
+                           na.strings = c("0", "NA"),
+                           sep = '\t')
+
+    # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices 
+    group1_ind_file <- read.csv(args[2], header = FALSE)[1, ]
+    group2_ind_file <- read.csv(args[3], header = FALSE)[1, ]
+
+    # read 4th argument, which is output file name
+    out_file <- args[4]
+
+    # get vectors of column names
+    df_names <- colnames(quant_file)
+    group1_names <- df_names[group1_ind_file]
+    group2_names <- df_names[group2_ind_file]
+ 
+    # run PECA_df
+    # id column is first column (hard-coded)
+    results <- PECA_df(quant_file, group1_names, group2_names, id = df_names[1])
+
+    # put add protein names column
+    results$prot <- row.names(results)
+    results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")]
+ 
+    # write to output
+    write.table(results, file=out_file,
+               quote=FALSE,
+               sep ='\t', 
+               row.names = FALSE)
+}
+
+main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peca.xml	Wed Feb 21 16:29:34 2018 -0500
@@ -0,0 +1,30 @@
+<tool id="peca" name="PECA: Probe-level expression change averaging" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="1.14.0">bioconductor-peca</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ## write group 1 to file
+        echo '$group1' > group1.txt &&
+        echo '$group2' > group2.txt && 
+        cat group1.txt &&
+        Rscript --vanilla '$__tool_directory__/peca.R' '$input' '$group1' '$group2' '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular"/>
+        <param name="group1" type="data_column" data_ref="input" multiple="true"/>
+        <param name="group2" type="data_column" data_ref="input" multiple="true"/> 
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test.tab" ftype="tabular"/>
+            <param name="group1" value="2,3,4"/>
+            <param name="group2" value="4,5,6"/>
+            <output name="output" file="out.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group1.txt	Wed Feb 21 16:29:34 2018 -0500
@@ -0,0 +1,3 @@
+2
+3
+4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group2.txt	Wed Feb 21 16:29:34 2018 -0500
@@ -0,0 +1,3 @@
+5
+6
+7
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.tab	Wed Feb 21 16:29:34 2018 -0500
@@ -0,0 +1,4 @@
+prot	slr	t	score	n	p	p.fdr
+a	-0.111780781397145	-0.765478419573781	0.486657928314213	10	0.465522239154437	0.471387593353045
+b	-0.0722462577076137	-0.761219732287275	0.488931365477738	10	0.471387593353045	0.471387593353045
+c	-0.118399562851212	-1.87027001064663	0.134789006543826	10	0.00228835744682698	0.00686507234048095
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.tab	Wed Feb 21 16:29:34 2018 -0500
@@ -0,0 +1,31 @@
+id	A1	A2	A3	B1	B2	B3
+a	54.2489063734367	49.6390576576586	55.1240726937295	49.6144780991222	50.8330349763798	53.9514564709181
+a	60.3240661014468	42.2917145283503	59.0254299559973	53.405354969144	66.559743175806	49.9652107364224
+a	56.3635394881666	39.0147151139471	54.3682844939657	53.7991057027463	54.06753635305	48.6838484867888
+a	43.4176092858866	47.1876317055487	44.8487665751097	57.6965465932599	54.7681375214397	51.8326362250669
+a	50.0551194571448	54.2119721603887	49.2509701326719	47.8977896731825	48.8221265606082	54.4935355307123
+a	49.8505658819176	40.3299420230831	48.7279482143961	55.7828322268111	54.0747354590324	54.5984495122319
+a	44.4753502143705	43.7899054516062	53.4932583201426	57.6546852980842	52.017781728326	50.3053654532735
+a	59.4620167107059	53.4648876489429	44.7651094148184	48.4178737005459	54.6258851880828	46.1245327523094
+a	49.6179461331221	45.3094403486909	50.8916567199704	59.1464413710981	60.0390757911603	50.8562740751764
+a	46.887154804165	50.9510907893787	55.0989810208619	48.2730059942602	57.6733204553657	64.1399697781665
+b	43.7343463751954	46.3207426732163	48.2222516204486	49.5643102909139	50.6434003578977	41.9768075843575
+b	59.3746925324757	45.2600349715115	46.4319107034971	43.3647332795063	58.0205082314023	52.0813651368811
+b	57.5390314413131	39.27264669353	55.2446550784507	49.4255140747867	52.949041959725	54.6454658654733
+b	45.8948784060825	46.2305745583783	52.4810269007389	49.8644917420684	49.8623114124141	49.4526454470161
+b	52.3842608595992	53.9145069152949	55.3151221876286	58.5746717923502	54.4750458440023	58.0920256016475
+b	44.9334101981099	42.4876151894126	55.0331502351991	47.3331761490083	47.9044196647419	59.334366547243
+b	57.9587874641605	56.0037071555751	57.419404123409	59.1536543270164	57.1445603630244	40.8404059053939
+b	55.2984221223832	43.1361387542313	54.4834238275705	59.6634323192618	51.7794901922063	56.5759881835152
+b	48.9423537862295	47.4638767071427	48.2194814941879	51.7775721002268	54.6930699559996	51.9582668855074
+b	54.3118247934725	39.8728288965565	52.6890807019854	49.0590745676018	62.1038198899922	53.9137630946883
+c	41.7378981728219	42.1299586143566	56.2922128023528	46.6200805390419	57.8697908417515	43.9440844795336
+c	48.2165209169497	41.86126017411	44.6506966044542	56.023500646768	53.5923002494182	55.5790515614602
+c	47.3390756225799	50.6105245971985	46.7635281876903	49.9940888411278	50.7179013415607	49.3092549972827
+c	48.3265503600379	40.912793826118	55.1625115343392	47.0734086325775	58.1109095582307	50.1587083236597
+c	44.0575082382113	43.1555584797624	46.220563477779	50.0771152407653	62.1537891209805	51.0866411965226
+c	49.6692945076024	48.3588269901328	48.1081311356118	51.5803868735586	53.5273654780519	54.9831676591611
+c	46.9501612503767	47.6985425078114	57.2693928588069	49.6957244391895	47.9997391642407	52.241811304542
+c	49.1276885847386	36.7303899690904	32.4087180261451	51.211378081021	53.5484109656343	53.5542555368538
+c	49.7627390723602	43.5336839023677	46.5137096514578	51.149647420808	48.1099599398199	45.5035113563574
+c	43.9082401716298	42.2573039778399	48.5483133832217	47.9882282287463	50.2797890577276	52.1769388638489