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annotate vegan_macros.xml @ 1:dd2705a31239 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
author iuc
date Mon, 08 Feb 2016 15:24:42 -0500
parents 3d1d965b6423
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3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="3.2.1">R</requirement>
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5 <requirement type="package" version="2.3-0">vegan</requirement>
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6 <yield />
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7 </requirements>
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8 </xml>
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10 <xml name="version_command">
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11 <version_command><![CDATA[Rscript -e 'library(vegan)' 2>&1 > /dev/null | grep 'This is vegan']]></version_command>
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12 </xml>
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14 <xml name="stdio">
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15 <stdio>
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16 <exit_code range="1:" />
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17 <exit_code range=":-1" />
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18 </stdio>
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19 </xml>
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21 <xml name="params_load_tabular_file">
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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"/>
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23 <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
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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"/>
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25 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
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26 </xml>
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28 <token name="@RSCRIPT_LOAD_TABULAR_FILE@"><![CDATA[
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29 #set $int_species_column = int( str( $species_column ) )
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
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30 #set $fixed_sample_columns = []
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31 #for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
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32 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
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33 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
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34 #end for
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35 input_abundance <- read.delim("${input_abundance}", header=${header}, sep="\t", row.names=${ species_column })
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36 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
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37
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38 ]]>
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39 </token>
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41 <token name="@RSCRIPT_PREAMBLE@"><![CDATA[
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42 options(bitmapType='cairo')## No X11, so we'll use cairo
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43 library(vegan)
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44 ]]>
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45 </token>
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47 <token name="@VERSION@">2.3-0</token>
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48
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49 </macros>