Mercurial > repos > iuc > vegan_rarefaction

comparison macros.xml @ 2:b0d5976540e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 11:31:02 -0400
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children af1211ed6c8e
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1:dd2705a31239 2:b0d5976540e3
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">r-vegan</requirement>
5 <yield />
6 </requirements>
7 </xml>
8
9 <xml name="version_command">
10 <version_command><![CDATA[Rscript -e 'library(vegan)' 2>&1 > /dev/null | grep 'This is vegan']]></version_command>
11 </xml>
12
13 <xml name="stdio">
14 <stdio>
15 <exit_code range="1:" />
16 <exit_code range=":-1" />
17 </stdio>
18 </xml>
19
20 <xml name="params_load_tabular_file">
21 <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"/>
22 <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
23 <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"/>
24 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
25 </xml>
26
27 <token name="@RSCRIPT_LOAD_TABULAR_FILE@"><![CDATA[
28 #set $int_species_column = int( str( $species_column ) )
29 #set $fixed_sample_columns = []
30 #for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
31 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
32 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
33 #end for
34 input_abundance <- read.delim("${input_abundance}", header=${header}, sep="\t", row.names=${ species_column })
35 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
36
37 ]]>
38 </token>
39
40 <token name="@RSCRIPT_PREAMBLE@"><![CDATA[
41 options(bitmapType='cairo')## No X11, so we'll use cairo
42 library(vegan)
43 ]]>
44 </token>
45
46 <token name="@TOOL_VERSION@">2.4-3</token>
47
48 </macros>