| Next changeset 1:f1b7d0032530 (2018-09-11) |
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Commit message:
Uploaded |
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added:
tab2csv.R tab2csv.xml |
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| diff -r 000000000000 -r 659820e2aa61 tab2csv.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tab2csv.R Wed Aug 08 06:23:04 2018 -0400 |
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| @@ -0,0 +1,14 @@ +#!/usr/bin/env Rscript +#Read csv - return tabular +#2 Options for now : sep an header + +args = commandArgs(trailingOnly=TRUE) + +if(args[3]=="TRUE"){ + tabular<-read.table(args[1],sep="\t",header=TRUE) + write.tale(tabular,"out.csv",sep=args[2],row.names=FALSE) +}else{ + tabular<-read.table(args[1],sep="\t",header=FALSE) + write.table(tabular,"out.csv",sep=args[2],col.names=FALSE,row.names=FALSE) +} + |
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| diff -r 000000000000 -r 659820e2aa61 tab2csv.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tab2csv.xml Wed Aug 08 06:23:04 2018 -0400 |
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| @@ -0,0 +1,73 @@ +<tool id="tab2csv_R" name="Tabular to CSV" version="0.1"> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/tab2csv.R' '$input1' '$sep' '$header' '$output' ]]> + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="tabular file"/> + <param name="sep" type="text" label="output csv Separator" value=","> + <sanitizer sanitize="False"/> + </param> + <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Header in file"/> + + </inputs> + + <outputs> + <data format="csv" name="output" from_work_dir="out.csv" /> + </outputs> + + <tests> + <test> + <param name="input1" value="example_tab.tabular"/> + <param name="sep" value=","/> + <param name="header" value="FALSE"/> + <output name="output" file="out.csv"/> + </test> + </tests> + + <help> +**What it does** + +Convert a tabular file to a CSV. + +Transform the tabs to the chosen separator. It is important to specify if the file has a header line. + +------ + +**Example** + +Input tabular : + + "John" "Smith" "2 mySteet, myCity" + + "François" "LeFrançais" "1 rue du Général, Paris" + + "Other" "Random" "Stuff, stuff, stuff" + + +Output CSV : + + "John","Smith","2 mySteet, myCity" + + "François","LeFrançais","1 rue du Général, Paris" + + "Other","Random","Stuff, stuff, stuff" + + + + +------ + +**Arguments** + +Input : tabular file. + +Separator : default is ",". + +Header : True/False. + + + </help> +</tool> |