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comparison vegan_macros.xml @ 0:c58e19ff504a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit 0e04a4c237677c1f5be1950babcf8591097996a9
author iuc
date Wed, 23 Dec 2015 13:55:10 -0500
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children db56c8e79b1e
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-1:000000000000 0:c58e19ff504a
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="3.2.1">R</requirement>
5 <requirement type="package" version="2.3-0">vegan</requirement>
6 <yield />
7 </requirements>
8 </xml>
9
10 <xml name="version_command">
11 <version_command><![CDATA[Rscript -e 'library(vegan)' 2>&1 > /dev/null | grep 'This is vegan']]></version_command>
12 </xml>
13
14 <xml name="stdio">
15 <stdio>
16 <exit_code range="1:" />
17 <exit_code range=":-1" />
18 </stdio>
19 </xml>
20
21 <xml name="params_load_tabular_file">
22 <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"/>
23 <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
24 <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"/>
25 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
26 </xml>
27
28 <token name="@RSCRIPT_LOAD_TABULAR_FILE@"><![CDATA[
29 #set $int_species_column = int( str( $species_column ) )
30 #set $fixed_sample_columns = []
31 #for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
32 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
33 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
34 #end for
35 input_abundance <- read.delim("${input_abundance}", header=${header}, sep="\t", row.names=${ species_column })
36 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
37
38 ]]>
39 </token>
40
41 <token name="@RSCRIPT_PREAMBLE@"><![CDATA[
42 options(bitmapType='cairo')## No X11, so we'll use cairo
43 library(vegan)
44 ]]>
45 </token>
46
47 <token name="@VERSION@">2.3-0</token>
48
49 </macros>