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annotate r_wrapper.sh @ 3:319fa5a9fc1b draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
author devteam
date Wed, 07 Dec 2016 18:29:23 -0500
parents acf952549b53
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1 #!/bin/sh
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2
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319fa5a9fc1b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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3 ### Run R providing the R script in $1 as standard input and passing
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4 ### the remaining arguments on the command line
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5
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6 # Function that writes a message to stderr and exits
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7 function fail
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8 {
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9 echo "$@" >&2
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10 exit 1
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11 }
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12
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13 # Ensure R executable is found
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319fa5a9fc1b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot commit facdb350072c8492654c90040fea3109dc9b51cd
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14 which R > /dev/null || fail "'R' is required by this tool but was not found on path"
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15
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16 # Extract first argument
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17 infile=$1; shift
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18
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19 # Ensure the file exists
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20 test -f $infile || fail "R input file '$infile' does not exist"
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21
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22 # Invoke R passing file named by first argument to stdin
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23 R --vanilla --slave $* < $infile