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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2 commit 62172bde663955b6c3cb86dc22c47739824f014a |
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added:
cast.xml macros.xml test-data/cast_result1.tabular test-data/melt_result1.tabular test-data/mtcars.txt |
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| diff -r 000000000000 -r d3b66a3a08ca cast.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cast.xml Tue Aug 22 07:44:04 2017 -0400 |
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| @@ -0,0 +1,56 @@ +<tool id="cast" name="cast" version="@VERSION@"> + <description>expand combinations of variables:values to columnar format</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <command detect_errors="exit_code"><![CDATA[ +cat '$script' && +Rscript '$script' + ]]></command> + <configfiles> + <configfile name="script"><![CDATA[ +## Setup R error handling to go to stderr +options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +## Import library +library("reshape2") + +input <- read.csv('$input', sep='\t', header=TRUE) +cinput <- dcast(input, ... ~ variable) +write.table(cinput, "output.tabular", sep="\t", quote=FALSE, row.names=FALSE) + + ]]></configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="tabular" label="Input should be molten data"/> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="output.tabular"/> + </outputs> + <tests> + <test> + <param name="input" value="melt_result1.tabular"/> + <output name="output" file="cast_result1.tabular"/> + </test> + </tests> + <help><![CDATA[ +This tool will apply the dcast function of the reshape2 R package. The input data should be in a 'long' format or molten by the melt tool. The output will be in a wide format. +The cast function expands each unique variable:value combination on a single line to columnar format. Documantation on the reshape2 package can be found here: https://cran.r-project.org/web/packages/reshape2/reshape2.pdf + ]]></help> + <citations> + <citation type="bibtex"> +@Article{, + title = {Reshaping Data with the {reshape} Package}, + author = {Hadley Wickham}, + journal = {Journal of Statistical Software}, + year = {2007}, + volume = {21}, + number = {12}, + pages = {1--20}, + url = {http://www.jstatsoft.org/v21/i12/}, + } + </citation> + </citations> +</tool> |
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| diff -r 000000000000 -r d3b66a3a08ca macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 22 07:44:04 2017 -0400 |
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| @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">r-reshape2</requirement> + </requirements> + </xml> + <token name="@VERSION@">1.4.2</token> + +</macros> |
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| diff -r 000000000000 -r d3b66a3a08ca test-data/cast_result1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cast_result1.tabular Tue Aug 22 07:44:04 2017 -0400 |
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| @@ -0,0 +1,33 @@ +brand am carb cyl disp drat gear hp mpg qsec vs wt +AMC Javelin 0 2 8 304 3.15 3 150 15.2 17.3 0 3.435 +Cadillac Fleetwood 0 4 8 472 2.93 3 205 10.4 17.98 0 5.25 +Camaro Z28 0 4 8 350 3.73 3 245 13.3 15.41 0 3.84 +Chrysler Imperial 0 4 8 440 3.23 3 230 14.7 17.42 0 5.345 +Datsun 710 1 1 4 108 3.85 4 93 22.8 18.61 1 2.32 +Dodge Challenger 0 2 8 318 2.76 3 150 15.5 16.87 0 3.52 +Duster 360 0 4 8 360 3.21 3 245 14.3 15.84 0 3.57 +Ferrari Dino 1 6 6 145 3.62 5 175 19.7 15.5 0 2.77 +Fiat 128 1 1 4 78.7 4.08 4 66 32.4 19.47 1 2.2 +Fiat X1-9 1 1 4 79 4.08 4 66 27.3 18.9 1 1.935 +Ford Pantera L 1 4 8 351 4.22 5 264 15.8 14.5 0 3.17 +Honda Civic 1 2 4 75.7 4.93 4 52 30.4 18.52 1 1.615 +Hornet 4 Drive 0 1 6 258 3.08 3 110 21.4 19.44 1 3.215 +Hornet Sportabout 0 2 8 360 3.15 3 175 18.7 17.02 0 3.44 +Lincoln Continental 0 4 8 460 3 3 215 10.4 17.82 0 5.424 +Lotus Europa 1 2 4 95.1 3.77 5 113 30.4 16.9 1 1.513 +Maserati Bora 1 8 8 301 3.54 5 335 15 14.6 0 3.57 +Mazda RX4 1 4 6 160 3.9 4 110 21 16.46 0 2.62 +Mazda RX4 Wag 1 4 6 160 3.9 4 110 21 17.02 0 2.875 +Merc 230 0 2 4 140.8 3.92 4 95 22.8 22.9 1 3.15 +Merc 240D 0 2 4 146.7 3.69 4 62 24.4 20 1 3.19 +Merc 280 0 4 6 167.6 3.92 4 123 19.2 18.3 1 3.44 +Merc 280C 0 4 6 167.6 3.92 4 123 17.8 18.9 1 3.44 +Merc 450SE 0 3 8 275.8 3.07 3 180 16.4 17.4 0 4.07 +Merc 450SL 0 3 8 275.8 3.07 3 180 17.3 17.6 0 3.73 +Merc 450SLC 0 3 8 275.8 3.07 3 180 15.2 18 0 3.78 +Pontiac Firebird 0 2 8 400 3.08 3 175 19.2 17.05 0 3.845 +Porsche 914-2 1 2 4 120.3 4.43 5 91 26 16.7 0 2.14 +Toyota Corolla 1 1 4 71.1 4.22 4 65 33.9 19.9 1 1.835 +Toyota Corona 0 1 4 120.1 3.7 3 97 21.5 20.01 1 2.465 +Valiant 0 1 6 225 2.76 3 105 18.1 20.22 1 3.46 +Volvo 142E 1 2 4 121 4.11 4 109 21.4 18.6 1 2.78 |
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| diff -r 000000000000 -r d3b66a3a08ca test-data/melt_result1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/melt_result1.tabular Tue Aug 22 07:44:04 2017 -0400 |
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| @@ -0,0 +1,353 @@ +brand variable value +Mazda RX4 mpg 21 +Mazda RX4 Wag mpg 21 +Datsun 710 mpg 22.8 +Hornet 4 Drive mpg 21.4 +Hornet Sportabout mpg 18.7 +Valiant mpg 18.1 +Duster 360 mpg 14.3 +Merc 240D mpg 24.4 +Merc 230 mpg 22.8 +Merc 280 mpg 19.2 +Merc 280C mpg 17.8 +Merc 450SE mpg 16.4 +Merc 450SL mpg 17.3 +Merc 450SLC mpg 15.2 +Cadillac Fleetwood mpg 10.4 +Lincoln Continental mpg 10.4 +Chrysler Imperial mpg 14.7 +Fiat 128 mpg 32.4 +Honda Civic mpg 30.4 +Toyota Corolla mpg 33.9 +Toyota Corona mpg 21.5 +Dodge Challenger mpg 15.5 +AMC Javelin mpg 15.2 +Camaro Z28 mpg 13.3 +Pontiac Firebird mpg 19.2 +Fiat X1-9 mpg 27.3 +Porsche 914-2 mpg 26 +Lotus Europa mpg 30.4 +Ford Pantera L mpg 15.8 +Ferrari Dino mpg 19.7 +Maserati Bora mpg 15 +Volvo 142E mpg 21.4 +Mazda RX4 cyl 6 +Mazda RX4 Wag cyl 6 +Datsun 710 cyl 4 +Hornet 4 Drive cyl 6 +Hornet Sportabout cyl 8 +Valiant cyl 6 +Duster 360 cyl 8 +Merc 240D cyl 4 +Merc 230 cyl 4 +Merc 280 cyl 6 +Merc 280C cyl 6 +Merc 450SE cyl 8 +Merc 450SL cyl 8 +Merc 450SLC cyl 8 +Cadillac Fleetwood cyl 8 +Lincoln Continental cyl 8 +Chrysler Imperial cyl 8 +Fiat 128 cyl 4 +Honda Civic cyl 4 +Toyota Corolla cyl 4 +Toyota Corona cyl 4 +Dodge Challenger cyl 8 +AMC Javelin cyl 8 +Camaro Z28 cyl 8 +Pontiac Firebird cyl 8 +Fiat X1-9 cyl 4 +Porsche 914-2 cyl 4 +Lotus Europa cyl 4 +Ford Pantera L cyl 8 +Ferrari Dino cyl 6 +Maserati Bora cyl 8 +Volvo 142E cyl 4 +Mazda RX4 disp 160 +Mazda RX4 Wag disp 160 +Datsun 710 disp 108 +Hornet 4 Drive disp 258 +Hornet Sportabout disp 360 +Valiant disp 225 +Duster 360 disp 360 +Merc 240D disp 146.7 +Merc 230 disp 140.8 +Merc 280 disp 167.6 +Merc 280C disp 167.6 +Merc 450SE disp 275.8 +Merc 450SL disp 275.8 +Merc 450SLC disp 275.8 +Cadillac Fleetwood disp 472 +Lincoln Continental disp 460 +Chrysler Imperial disp 440 +Fiat 128 disp 78.7 +Honda Civic disp 75.7 +Toyota Corolla disp 71.1 +Toyota Corona disp 120.1 +Dodge Challenger disp 318 +AMC Javelin disp 304 +Camaro Z28 disp 350 +Pontiac Firebird disp 400 +Fiat X1-9 disp 79 +Porsche 914-2 disp 120.3 +Lotus Europa disp 95.1 +Ford Pantera L disp 351 +Ferrari Dino disp 145 +Maserati Bora disp 301 +Volvo 142E disp 121 +Mazda RX4 hp 110 +Mazda RX4 Wag hp 110 +Datsun 710 hp 93 +Hornet 4 Drive hp 110 +Hornet Sportabout hp 175 +Valiant hp 105 +Duster 360 hp 245 +Merc 240D hp 62 +Merc 230 hp 95 +Merc 280 hp 123 +Merc 280C hp 123 +Merc 450SE hp 180 +Merc 450SL hp 180 +Merc 450SLC hp 180 +Cadillac Fleetwood hp 205 +Lincoln Continental hp 215 +Chrysler Imperial hp 230 +Fiat 128 hp 66 +Honda Civic hp 52 +Toyota Corolla hp 65 +Toyota Corona hp 97 +Dodge Challenger hp 150 +AMC Javelin hp 150 +Camaro Z28 hp 245 +Pontiac Firebird hp 175 +Fiat X1-9 hp 66 +Porsche 914-2 hp 91 +Lotus Europa hp 113 +Ford Pantera L hp 264 +Ferrari Dino hp 175 +Maserati Bora hp 335 +Volvo 142E hp 109 +Mazda RX4 drat 3.9 +Mazda RX4 Wag drat 3.9 +Datsun 710 drat 3.85 +Hornet 4 Drive drat 3.08 +Hornet Sportabout drat 3.15 +Valiant drat 2.76 +Duster 360 drat 3.21 +Merc 240D drat 3.69 +Merc 230 drat 3.92 +Merc 280 drat 3.92 +Merc 280C drat 3.92 +Merc 450SE drat 3.07 +Merc 450SL drat 3.07 +Merc 450SLC drat 3.07 +Cadillac Fleetwood drat 2.93 +Lincoln Continental drat 3 +Chrysler Imperial drat 3.23 +Fiat 128 drat 4.08 +Honda Civic drat 4.93 +Toyota Corolla drat 4.22 +Toyota Corona drat 3.7 +Dodge Challenger drat 2.76 +AMC Javelin drat 3.15 +Camaro Z28 drat 3.73 +Pontiac Firebird drat 3.08 +Fiat X1-9 drat 4.08 +Porsche 914-2 drat 4.43 +Lotus Europa drat 3.77 +Ford Pantera L drat 4.22 +Ferrari Dino drat 3.62 +Maserati Bora drat 3.54 +Volvo 142E drat 4.11 +Mazda RX4 wt 2.62 +Mazda RX4 Wag wt 2.875 +Datsun 710 wt 2.32 +Hornet 4 Drive wt 3.215 +Hornet Sportabout wt 3.44 +Valiant wt 3.46 +Duster 360 wt 3.57 +Merc 240D wt 3.19 +Merc 230 wt 3.15 +Merc 280 wt 3.44 +Merc 280C wt 3.44 +Merc 450SE wt 4.07 +Merc 450SL wt 3.73 +Merc 450SLC wt 3.78 +Cadillac Fleetwood wt 5.25 +Lincoln Continental wt 5.424 +Chrysler Imperial wt 5.345 +Fiat 128 wt 2.2 +Honda Civic wt 1.615 +Toyota Corolla wt 1.835 +Toyota Corona wt 2.465 +Dodge Challenger wt 3.52 +AMC Javelin wt 3.435 +Camaro Z28 wt 3.84 +Pontiac Firebird wt 3.845 +Fiat X1-9 wt 1.935 +Porsche 914-2 wt 2.14 +Lotus Europa wt 1.513 +Ford Pantera L wt 3.17 +Ferrari Dino wt 2.77 +Maserati Bora wt 3.57 +Volvo 142E wt 2.78 +Mazda RX4 qsec 16.46 +Mazda RX4 Wag qsec 17.02 +Datsun 710 qsec 18.61 +Hornet 4 Drive qsec 19.44 +Hornet Sportabout qsec 17.02 +Valiant qsec 20.22 +Duster 360 qsec 15.84 +Merc 240D qsec 20 +Merc 230 qsec 22.9 +Merc 280 qsec 18.3 +Merc 280C qsec 18.9 +Merc 450SE qsec 17.4 +Merc 450SL qsec 17.6 +Merc 450SLC qsec 18 +Cadillac Fleetwood qsec 17.98 +Lincoln Continental qsec 17.82 +Chrysler Imperial qsec 17.42 +Fiat 128 qsec 19.47 +Honda Civic qsec 18.52 +Toyota Corolla qsec 19.9 +Toyota Corona qsec 20.01 +Dodge Challenger qsec 16.87 +AMC Javelin qsec 17.3 +Camaro Z28 qsec 15.41 +Pontiac Firebird qsec 17.05 +Fiat X1-9 qsec 18.9 +Porsche 914-2 qsec 16.7 +Lotus Europa qsec 16.9 +Ford Pantera L qsec 14.5 +Ferrari Dino qsec 15.5 +Maserati Bora qsec 14.6 +Volvo 142E qsec 18.6 +Mazda RX4 vs 0 +Mazda RX4 Wag vs 0 +Datsun 710 vs 1 +Hornet 4 Drive vs 1 +Hornet Sportabout vs 0 +Valiant vs 1 +Duster 360 vs 0 +Merc 240D vs 1 +Merc 230 vs 1 +Merc 280 vs 1 +Merc 280C vs 1 +Merc 450SE vs 0 +Merc 450SL vs 0 +Merc 450SLC vs 0 +Cadillac Fleetwood vs 0 +Lincoln Continental vs 0 +Chrysler Imperial vs 0 +Fiat 128 vs 1 +Honda Civic vs 1 +Toyota Corolla vs 1 +Toyota Corona vs 1 +Dodge Challenger vs 0 +AMC Javelin vs 0 +Camaro Z28 vs 0 +Pontiac Firebird vs 0 +Fiat X1-9 vs 1 +Porsche 914-2 vs 0 +Lotus Europa vs 1 +Ford Pantera L vs 0 +Ferrari Dino vs 0 +Maserati Bora vs 0 +Volvo 142E vs 1 +Mazda RX4 am 1 +Mazda RX4 Wag am 1 +Datsun 710 am 1 +Hornet 4 Drive am 0 +Hornet Sportabout am 0 +Valiant am 0 +Duster 360 am 0 +Merc 240D am 0 +Merc 230 am 0 +Merc 280 am 0 +Merc 280C am 0 +Merc 450SE am 0 +Merc 450SL am 0 +Merc 450SLC am 0 +Cadillac Fleetwood am 0 +Lincoln Continental am 0 +Chrysler Imperial am 0 +Fiat 128 am 1 +Honda Civic am 1 +Toyota Corolla am 1 +Toyota Corona am 0 +Dodge Challenger am 0 +AMC Javelin am 0 +Camaro Z28 am 0 +Pontiac Firebird am 0 +Fiat X1-9 am 1 +Porsche 914-2 am 1 +Lotus Europa am 1 +Ford Pantera L am 1 +Ferrari Dino am 1 +Maserati Bora am 1 +Volvo 142E am 1 +Mazda RX4 gear 4 +Mazda RX4 Wag gear 4 +Datsun 710 gear 4 +Hornet 4 Drive gear 3 +Hornet Sportabout gear 3 +Valiant gear 3 +Duster 360 gear 3 +Merc 240D gear 4 +Merc 230 gear 4 +Merc 280 gear 4 +Merc 280C gear 4 +Merc 450SE gear 3 +Merc 450SL gear 3 +Merc 450SLC gear 3 +Cadillac Fleetwood gear 3 +Lincoln Continental gear 3 +Chrysler Imperial gear 3 +Fiat 128 gear 4 +Honda Civic gear 4 +Toyota Corolla gear 4 +Toyota Corona gear 3 +Dodge Challenger gear 3 +AMC Javelin gear 3 +Camaro Z28 gear 3 +Pontiac Firebird gear 3 +Fiat X1-9 gear 4 +Porsche 914-2 gear 5 +Lotus Europa gear 5 +Ford Pantera L gear 5 +Ferrari Dino gear 5 +Maserati Bora gear 5 +Volvo 142E gear 4 +Mazda RX4 carb 4 +Mazda RX4 Wag carb 4 +Datsun 710 carb 1 +Hornet 4 Drive carb 1 +Hornet Sportabout carb 2 +Valiant carb 1 +Duster 360 carb 4 +Merc 240D carb 2 +Merc 230 carb 2 +Merc 280 carb 4 +Merc 280C carb 4 +Merc 450SE carb 3 +Merc 450SL carb 3 +Merc 450SLC carb 3 +Cadillac Fleetwood carb 4 +Lincoln Continental carb 4 +Chrysler Imperial carb 4 +Fiat 128 carb 1 +Honda Civic carb 2 +Toyota Corolla carb 1 +Toyota Corona carb 1 +Dodge Challenger carb 2 +AMC Javelin carb 2 +Camaro Z28 carb 4 +Pontiac Firebird carb 2 +Fiat X1-9 carb 1 +Porsche 914-2 carb 2 +Lotus Europa carb 2 +Ford Pantera L carb 4 +Ferrari Dino carb 6 +Maserati Bora carb 8 +Volvo 142E carb 2 |
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| diff -r 000000000000 -r d3b66a3a08ca test-data/mtcars.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mtcars.txt Tue Aug 22 07:44:04 2017 -0400 |
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| @@ -0,0 +1,33 @@ +brand mpg cyl disp hp drat wt qsec vs am gear carb +Mazda RX4 21 6 160 110 3.9 2.62 16.46 0 1 4 4 +Mazda RX4 Wag 21 6 160 110 3.9 2.875 17.02 0 1 4 4 +Datsun 710 22.8 4 108 93 3.85 2.32 18.61 1 1 4 1 +Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 +Hornet Sportabout 18.7 8 360 175 3.15 3.44 17.02 0 0 3 2 +Valiant 18.1 6 225 105 2.76 3.46 20.22 1 0 3 1 +Duster 360 14.3 8 360 245 3.21 3.57 15.84 0 0 3 4 +Merc 240D 24.4 4 146.7 62 3.69 3.19 20 1 0 4 2 +Merc 230 22.8 4 140.8 95 3.92 3.15 22.9 1 0 4 2 +Merc 280 19.2 6 167.6 123 3.92 3.44 18.3 1 0 4 4 +Merc 280C 17.8 6 167.6 123 3.92 3.44 18.9 1 0 4 4 +Merc 450SE 16.4 8 275.8 180 3.07 4.07 17.4 0 0 3 3 +Merc 450SL 17.3 8 275.8 180 3.07 3.73 17.6 0 0 3 3 +Merc 450SLC 15.2 8 275.8 180 3.07 3.78 18 0 0 3 3 +Cadillac Fleetwood 10.4 8 472 205 2.93 5.25 17.98 0 0 3 4 +Lincoln Continental 10.4 8 460 215 3 5.424 17.82 0 0 3 4 +Chrysler Imperial 14.7 8 440 230 3.23 5.345 17.42 0 0 3 4 +Fiat 128 32.4 4 78.7 66 4.08 2.2 19.47 1 1 4 1 +Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 +Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.9 1 1 4 1 +Toyota Corona 21.5 4 120.1 97 3.7 2.465 20.01 1 0 3 1 +Dodge Challenger 15.5 8 318 150 2.76 3.52 16.87 0 0 3 2 +AMC Javelin 15.2 8 304 150 3.15 3.435 17.3 0 0 3 2 +Camaro Z28 13.3 8 350 245 3.73 3.84 15.41 0 0 3 4 +Pontiac Firebird 19.2 8 400 175 3.08 3.845 17.05 0 0 3 2 +Fiat X1-9 27.3 4 79 66 4.08 1.935 18.9 1 1 4 1 +Porsche 914-2 26 4 120.3 91 4.43 2.14 16.7 0 1 5 2 +Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.9 1 1 5 2 +Ford Pantera L 15.8 8 351 264 4.22 3.17 14.5 0 1 5 4 +Ferrari Dino 19.7 6 145 175 3.62 2.77 15.5 0 1 5 6 +Maserati Bora 15 8 301 335 3.54 3.57 14.6 0 1 5 8 +Volvo 142E 21.4 4 121 109 4.11 2.78 18.6 1 1 4 2 |