Mercurial > repos > devteam > vegan_rarefaction
changeset 1:da3fbdaaec5b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/vegan_rarefaction commit f28e850b6791f352750f23956d692aa835fc42af
| author | devteam |
|---|---|
| date | Wed, 26 Aug 2015 17:19:25 -0400 |
| parents | cc2380c0cf10 |
| children | |
| files | vegan_rarefaction.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- 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"/>