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comparison vegan_rarefaction.xml @ 1:da3fbdaaec5b draft default tip

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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
comparison
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0:cc2380c0cf10 1:da3fbdaaec5b
8 </requirements> 8 </requirements>
9 <stdio> 9 <stdio>
10 <exit_code range="1:" /> 10 <exit_code range="1:" />
11 <exit_code range=":-1" /> 11 <exit_code range=":-1" />
12 </stdio> 12 </stdio>
13
14 <command><![CDATA[ 13 <command><![CDATA[
15 #if "output_r_script" in str( $include_outputs ).split( "," ): 14 #if "output_r_script" in str( $include_outputs ).split( "," ):
16 cp "${vegan_rarefaction_script}" "${output_r_script}" && 15 cp "${vegan_rarefaction_script}" "${output_r_script}" &&
17 #end if 16 #end if
18 Rscript "${vegan_rarefaction_script}" 17 Rscript "${vegan_rarefaction_script}"
27 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same." 26 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
28 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) ) 27 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
29 #end for 28 #end for
30 options(bitmapType='cairo')## No X11, so we'll use cairo 29 options(bitmapType='cairo')## No X11, so we'll use cairo
31 library(vegan) 30 library(vegan)
32 input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=FALSE ) 31 input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=${header} )
33 32
34 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] ) 33 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
35 34
36 #if str( $sample_size ) == '': 35 #if str( $sample_size ) == '':
37 raremax <- min(rowSums(input_abundance)) 36 raremax <- min(rowSums(input_abundance))
74 </configfiles> 73 </configfiles>
75 <inputs> 74 <inputs>
76 <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"/> 75 <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"/>
77 <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/> 76 <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
78 <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"/> 77 <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"/>
78 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
79 <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."/> 79 <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."/>
80 <param name="step_size" type="integer" value="1" min="1" label="Step size for sample sizes"/> 80 <param name="step_size" type="integer" value="1" min="1" label="Step size for sample sizes"/>
81 <param name="xlab" type="text" value="Sample Size" label="X-axis label"/> 81 <param name="xlab" type="text" value="Sample Size" label="X-axis label"/>
82 <param name="ylab" type="text" value="Species" label="Y-axis label"/> 82 <param name="ylab" type="text" value="Species" label="Y-axis label"/>
83 <param name="label" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Label rarefaction curves by rownames of X"/> 83 <param name="label" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Label rarefaction curves by rownames of X"/>