| Previous changeset 30:dd947d71408e (2018-12-06) Next changeset 32:c23ad148d574 (2018-12-06) |
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Commit message:
Uploaded |
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added:
xlsx2tab/test-data/example_xlsx.xlsx xlsx2tab/xls2tab.R xlsx2tab/xls2tab.xml |
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removed:
xls2tab.R xls2tab.xml |
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| diff -r dd947d71408e -r eaaaa5d9aa4e xls2tab.R --- a/xls2tab.R Thu Dec 06 12:43:46 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -#!/usr/bin/env Rscript -#Read xls/xlsx sheets - return tabular -library(readxl) - -args = commandArgs(trailingOnly=TRUE) - -sheet<-read_excel(args[1],sheet=args[2]) -write.table(sheet,"out.tabular",sep="\t",row.names=FALSE) \ No newline at end of file |
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| diff -r dd947d71408e -r eaaaa5d9aa4e xls2tab.xml --- a/xls2tab.xml Thu Dec 06 12:43:46 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,55 +0,0 @@ -<tool id="xls2tab_R" name="XLS sheet to Tabular" version="0.1"> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - <requirement type="package" version="1.1.0">r-readxl</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - Rscript '$__tool_directory__/xls2tab.R' '$input1' '$sheet' '$output' ]]> - </command> - <inputs> - <param format="excel.xls,xlsx" name="input1" type="data" label="XLS/XLSX file"/> - <param name="sheet" type="text" label="Excel sheet name" value="biodiv_data"> - <sanitizer sanitize="False"/> - </param> - - </inputs> - - <outputs> - <data format="tabular" name="output" from_work_dir="out.tabular" /> - </outputs> - - <tests> - <test> - <param name="input1" value="example_xlsx.xlsx"/> - <param name="sheet" value="data"/> - <output name="output" file="out.tabular"/> - </test> - </tests> - - <help> -**What it does** - -Extract a sheet from XLS/XLSX file to a tabular file. - - ------- - -**Example** - -Input XLS/XLSX with a sheet named 'données in situ' - -Output tabular - - ------- - -**Arguments** - -Input: xls/xlsx file. -Excel sheet name: données in situ - - - - - </help> -</tool> |
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| diff -r dd947d71408e -r eaaaa5d9aa4e xlsx2tab/test-data/example_xlsx.xlsx |
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| Binary file xlsx2tab/test-data/example_xlsx.xlsx has changed |
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| diff -r dd947d71408e -r eaaaa5d9aa4e xlsx2tab/xls2tab.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xlsx2tab/xls2tab.R Thu Dec 06 12:52:35 2018 -0500 |
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| @@ -0,0 +1,8 @@ +#!/usr/bin/env Rscript +#Read xls/xlsx sheets - return tabular +library(readxl) + +args = commandArgs(trailingOnly=TRUE) + +sheet<-read_excel(args[1],sheet=args[2]) +write.table(sheet,"out.tabular",sep="\t",row.names=FALSE) \ No newline at end of file |
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| diff -r dd947d71408e -r eaaaa5d9aa4e xlsx2tab/xls2tab.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xlsx2tab/xls2tab.xml Thu Dec 06 12:52:35 2018 -0500 |
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| @@ -0,0 +1,55 @@ +<tool id="xls2tab_R" name="XLS sheet to Tabular" version="0.1"> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.1.0">r-readxl</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/xls2tab.R' '$input1' '$sheet' '$output' ]]> + </command> + <inputs> + <param format="excel.xls,xlsx" name="input1" type="data" label="XLS/XLSX file"/> + <param name="sheet" type="text" label="Excel sheet name" value="biodiv_data"> + <sanitizer sanitize="False"/> + </param> + + </inputs> + + <outputs> + <data format="tabular" name="output" from_work_dir="out.tabular" /> + </outputs> + + <tests> + <test> + <param name="input1" value="example_xlsx.xlsx"/> + <param name="sheet" value="data"/> + <output name="output" file="out.tabular"/> + </test> + </tests> + + <help> +**What it does** + +Extract a sheet from XLS/XLSX file to a tabular file. + + +------ + +**Example** + +Input XLS/XLSX with a sheet named 'données in situ' + +Output tabular + + +------ + +**Arguments** + +Input: xls/xlsx file. +Excel sheet name: données in situ + + + + + </help> +</tool> |