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annotate vegan_rarefaction.xml @ 0:cc2380c0cf10 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/packages/vegan_rarefaction commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty
author devteam
date Mon, 24 Aug 2015 10:55:33 -0400
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cc2380c0cf10 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/packages/vegan_rarefaction commit 5ad726dc73203a704666033cd3bf70b82575978f-dirty
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1 <tool id="vegan_rarefaction" name="Vegan Rarefaction" version="0.0.1">
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2 <description>
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3 curve and statistics
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="3.2.1">R</requirement>
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7 <requirement type="package" version="2.3-0">vegan</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
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13
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14 <command><![CDATA[
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15 #if "output_r_script" in str( $include_outputs ).split( "," ):
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16 cp "${vegan_rarefaction_script}" "${output_r_script}" &&
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17 #end if
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18 Rscript "${vegan_rarefaction_script}"
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19 ]]>
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20 </command>
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21 <configfiles>
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22 <configfile name="vegan_rarefaction_script"><![CDATA[
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23 #set $include_files = str( $include_outputs ).split( "," )
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24 #set $int_species_column = int( str( $species_column ) )
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25 #set $fixed_sample_columns = []
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26 #for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
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27 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
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28 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
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29 #end for
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30 options(bitmapType='cairo')## No X11, so we'll use cairo
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31 library(vegan)
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32 input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=FALSE )
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33
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34 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
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35
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36 #if str( $sample_size ) == '':
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37 raremax <- min(rowSums(input_abundance))
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38 raremax_offset <- -1
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39 sprintf("Automatically determining subsampling size, will apply offset to slope calculation and species probabilities.")
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40 #else:
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41 raremax = $sample_size
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42 raremax_offset <- 0
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43 #end if
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44 sprintf("Using sample size: %i", raremax)
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45 Srare <- rarefy(input_abundance, sample=raremax, se=FALSE, MARGIN=1)
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46 #if "output_richness" in $include_files:
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47 write.table(Srare, "${output_richness}", col.names=NA, sep = "\t")
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48 #end if
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49
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50 #if "output_slope" in $include_files:
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51 write.table(rareslope(input_abundance, sample=raremax+raremax_offset), "${output_slope}", sep = "\t")
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52 #end if
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53
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54 S <- specnumber(input_abundance)
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55 #if "output_species_count" in $include_files:
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56 write.table(S, "${ output_species_count }", col.names=NA, sep="\t" )
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57 #end if
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58
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59 #if "output_species_frequency" in $include_files:
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60 write.table(specnumber(input_abundance, MARGIN=2), "${ output_species_frequency }", col.names=NA, sep="\t" )
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61 #end if
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62
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63 #if "output_species_probabilities" in $include_files:
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64 write.table(drarefy(input_abundance, sample=raremax+raremax_offset), "${ output_species_probabilities }", col.names=NA, sep="\t" )
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65 #end if
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66
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67 #if "output_plot" in $include_files:
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68 png('${output_plot}', width=1020, height=800, units='px')
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69 rarecurve(input_abundance, step = ${step_size}, sample = raremax, xlab = "${xlab}", ylab = "${ylab}", label="${label}", col = "blue", cex = 0.6)
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70 invisible(dev.off())
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71 #end if
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72 ]]>
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73 </configfile>
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74 </configfiles>
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75 <inputs>
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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"/>
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77 <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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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"/>
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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."/>
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80 <param name="step_size" type="integer" value="1" min="1" label="Step size for sample sizes"/>
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81 <param name="xlab" type="text" value="Sample Size" label="X-axis label"/>
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82 <param name="ylab" type="text" value="Species" label="Y-axis label"/>
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83 <param name="label" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Label rarefaction curves by rownames of X"/>
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84 <param name="include_outputs" type="select" multiple="True" label="Datasets to create">
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85 <option value="output_species_count" selected="true">Count of species</option>
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86 <option value="output_species_frequency" selected="true">Species frequency</option>
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87 <option value="output_richness" selected="true">Richness</option>
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88 <option value="output_species_probabilities" selected="true">Species probabilities</option>
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89 <option value="output_slope" selected="true">Slope of rarefaction curve</option>
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90 <option value="output_r_script" selected="false">R script</option>
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91 <option value="output_plot" selected="true">Rarefaction plot</option>
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92 </param>
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93 </inputs>
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94 <outputs>
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95 <data format="tabular" name="output_species_count" label="${tool.name} on ${on_string} (number of species)">
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96 <filter>"output_species_count" in include_outputs</filter>
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97 </data>
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98 <data format="tabular" name="output_species_frequency" label="${tool.name} on ${on_string} (frequency of species)">
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99 <filter>"output_species_frequency" in include_outputs</filter>
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100 </data>
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101 <data format="tabular" name="output_richness" label="${tool.name} on ${on_string} (estimated richness)">
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102 <filter>"output_richness" in include_outputs</filter>
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103 </data>
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104 <data format="tabular" name="output_species_probabilities" label="${tool.name} on ${on_string} (species probabilities)">
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105 <filter>"output_species_probabilities" in include_outputs</filter>
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106 </data>
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107 <data format="tabular" name="output_slope" label="${tool.name} on ${on_string} (slope of curve)">
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108 <filter>"output_slope" in include_outputs</filter>
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109 </data>
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110 <data format="txt" name="output_r_script" label="${tool.name} on ${on_string} (Rscript)">
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111 <filter>"output_r_script" in include_outputs</filter>
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112 </data>
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113 <data format="png" name="output_plot" label="${tool.name} on ${on_string} (plot)">
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114 <filter>"output_plot" in include_outputs</filter>
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115 </data>
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116 </outputs>
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117 <tests>
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118 <test>
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119 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
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120 <param name="species_column" value="6"/>
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121 <param name="sample_columns" value="2"/>
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122 <param name="sample_size" value=""/>
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123 <param name="step_size" value="1"/>
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124 <param name="xlab" value="Sample Size"/>
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125 <param name="ylab" value="Species"/>
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126 <param name="label" value="TRUE"/>
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127 <output name="output_species_count" ftype="tabular" file="vegan_output_species_count.tabular" />
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128 <output name="output_species_frequency" ftype="tabular" file="vegan_output_species_frequency.tabular" />
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129 <output name="output_richness" ftype="tabular" file="vegan_output_richness.tabular" />
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130 <output name="output_species_probabilities" ftype="tabular" file="vegan_output_species_probabilities.tabular" />
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131 <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" />
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132 </test>
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133 </tests>
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134 <help>
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135 <![CDATA[
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136
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137 Gives the expected species richness in random subsamples of size sample from the community. The size of sample should be smaller than total community size, but the function will work for larger sample as well (with a warning) and return non-rarefied species richness (and standard error = 0). Rarefaction can be performed only with genuine counts of individuals. The function rarefy is based on Hurlbert’s (1971) formulation, and the standard errors on Heck et al. (1975).
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138
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139 Returns probabilities that species occur in a rarefied community of size sample.
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140
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141 Draws a rarefaction curve for each row of the input data. The rarefaction curves are evaluated using the interval of step sample sizes, always including 1 and total sample size. If sample is specified, a vertical line is drawn at sample with horizontal lines for the rarefied species richnesses.
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142
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143
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144 .. class:: warningmark
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145
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146 When subsampling by community size, slope of the rarefaction curve and species probabilities are computed using community size-1
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147 ]]>
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148 </help>
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149 <citations>
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150 </citations>
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151 </tool>