# HG changeset patch
# User devteam
# Date 1440623965 14400
# Node ID da3fbdaaec5bb17c9c8ac98e02a8e142cdf746c9
# Parent  cc2380c0cf10acd970dbb736eab425e66a95a6e5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/vegan_rarefaction commit f28e850b6791f352750f23956d692aa835fc42af

diff -r cc2380c0cf10 -r da3fbdaaec5b vegan_rarefaction.xml
--- a/vegan_rarefaction.xml	Mon Aug 24 10:55:33 2015 -0400
+++ b/vegan_rarefaction.xml	Wed Aug 26 17:19:25 2015 -0400
@@ -10,7 +10,6 @@
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
-
     <command><![CDATA[
         #if "output_r_script" in str( $include_outputs ).split( "," ):
             cp "${vegan_rarefaction_script}" "${output_r_script}" &&
@@ -29,7 +28,7 @@
 #end for
 options(bitmapType='cairo')## No X11, so we'll use cairo
 library(vegan)
-input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=FALSE )
+input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=${header} )
 
 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
 
@@ -76,6 +75,7 @@
         <param name="input_abundance" type="data" format="tabular" label="File with abundance values for community" help="Rows are samples; columns are species/phyla/community classifier"/>
         <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
         <param name="sample_columns" label="Sample count columns" type="data_column" multiple="True" value="2" data_ref="input_abundance" help="Select each column that contains counts"/>
+        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
         <param name="sample_size" type="integer" value="" min="1" optional="True" label="Subsample size for rarefying community" help="Leave empty to subsample by community size for the smallest sample."/>
         <param name="step_size" type="integer" value="1" min="1" label="Step size for sample sizes"/>
         <param name="xlab" type="text" value="Sample Size" label="X-axis label"/>