Mercurial > repos > iuc > ampvis2_ordinate

annotate ordinate.xml @ 4:e925f68abf2c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 commit e0ad9ce8f508215ec6af69be2682a0faf38415da
author iuc
date Mon, 10 Nov 2025 12:50:31 +0000
parents 918c4abfacf4
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918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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1 <tool id="ampvis2_ordinate" name="ampvis2 ordination plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="distmeasure_macro">
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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6 <param argument="distmeasure" type="select" label="Distance measure">
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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7 <option value="wunifrac">Weighted UniFrac. Requires a rooted phylogenetic tree.</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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8 <option value="unifrac">Unweighted UniFrac. Requires a phylogenetic tree.</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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9 <option value="jsd">Jensen-Shannon Divergence</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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10 <option value="manhattan">manhattan</option>
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11 <option value="euclidean">euclidean</option>
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12 <option value="canberra">canberra</option>
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13 <option value="bray" selected="true">bray</option>
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14 <option value="kulczynski">kulczynski</option>
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15 <option value="jaccard">jaccard</option>
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16 <option value="gower">gower</option>
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17 <option value="altGower">altGower</option>
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18 <option value="morisita">morisita</option>
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19 <option value="horn">horn</option>
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20 <option value="mountford">mountford</option>
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21 <option value="raup">raup</option>
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22 <option value="binomial">binomial</option>
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23 <option value="chao">chao</option>
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24 <option value="cao">cao</option>
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25 <option value="mahalanobis">mahalanobis</option>
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26 <option value="clark">Clark</option>
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27 <option value="chisq">Chi-square</option>
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28 <option value="chord"> Chord</option>
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29 <option value="hellinger">Hellinger</option>
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30 <option value="aitchison">Aitchison</option>
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31 <option value="robust.aitchison">Robust Aitchison </option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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32 </param>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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33 </xml>
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34 <!-- default is most often hellinger, but for N/MMDS none is suggested -->
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35 <xml name="transform_macro">
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 <param argument="transform" type="select" label="Transforms the abundances before ordination" help="See details in decostand. Using the hellinger transformation is a good choice when performing PCA/RDA as it will produce a more ecologically meaningful result (read about the double-zero problem in Numerical Ecology). When the Hellinger transformation is used with CA/CCA it will help reducing the impact of low abundant species. When performing nMDS or PCoA (aka mMDS) it is not recommended to also use data transformation as this will obscure the chosen distance measure.">
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 <option value="none">No transformation</option>
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38 <option value="total">divide by margin total (total)</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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39 <option value="max">divide by margin maximum (max)</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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40 <option value="freq">divide by margin total and multiply by the number of non-zero items, so that the average of non-zero entries is one (freq)</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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41 <option value="normalize">make margin sum of squares equal to one (normalize)</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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42 <option value="range">standardize values into range 0:1. If all values are constant, they will be transformed to 0. (range)</option>
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43 <option value="standardize">scale x to zero mean and unit variance (standardize)</option>
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44 <option value="pa">to presence/absence scale 0/1: absence/presence (pa)</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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45 <option value="chi.square">divide by row sums and square root of column sums, and adjust for square root of matrix total (chi.square)</option>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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46 <option value="hellinger">square root of method = "total" (hellinger)</option>
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47 <option value="log">logarithmic transformation (log)</option>
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48 <option value="sqrt">square root (sqrt)</option>
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49 </param>
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50 </xml>
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51 <xml name="transform_macro_hellinger">
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52 <expand macro="transform_macro">
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53 <option value="hellinger" selected="true">square root of method = "total" (hellinger)</option>
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54 </expand>
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55 </xml>
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56 <xml name="constrain_macro">
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57 <expand macro="metadata_select_discrete" argument="constrain" optional="false" multiple="true" label="Constrain analysis by" help="Variable(s) in the metadata for constrained analyses. Multiple variables can be provided, but keep in mind that the more variables selected the more the result will be similar to unconstrained analysis."/>
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58 </xml>
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59 </macros>
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60 <expand macro="header"/>
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61 <command detect_errors="exit_code"><![CDATA[
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62 Rscript '$rscript'
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63 ]]></command>
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64 <configfiles>
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65 <configfile name="rscript"><![CDATA[
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66 #if $type_cond.type in ['RDA', 'CCA'] and $type_cond.constrain
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67 #set constrain_list='c("' + '", "'.join(str($type_cond.constrain).split(",")) + '")'
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68 #else
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69 #set constrain_list='NULL'
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70 #end if
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71 library(ampvis2, quietly = TRUE)
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72 data <- readRDS("$data")
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73 details <- amp_ordinate(
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74 data,
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75 filter_species = $filter_species,
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76 type = "$type_cond.type",
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77 #if $type_cond.type in ['MMDS', 'NMDS']
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78 distmeasure = "$type_cond.distmeasure",
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79 #end if
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80 transform = "$type_cond.transform",
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81 #if $type_cond.type in ['RDA', 'CCA']
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82 constrain = $constrain_list,
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83 #end if
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84 ## x_axis = 1,
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85 ## y_axis = 2,
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86 print_caption = $print_caption,
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87 #if $sample_color_by
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88 sample_color_by = "$sample_color_by",
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89 #end if
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90 ## sample_color_order = NULL,
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91 #if $sample_shape_by
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92 sample_shape_by = "$sample_shape_by",
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93 #end if
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94 #if $sample_colorframe
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95 sample_colorframe = "$sample_colorframe",
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96 #end if
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97 #if $sample_colorframe_label
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98 sample_colorframe_label = "$sample_colorframe_label",
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99 #end if
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100 ## sample_colorframe_label_size = 3,
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101 #if $sample_label_by
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102 sample_label_by = "$sample_label_by",
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103 #end if
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104 ## sample_label_size = 4,
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105 ## sample_label_segment_color = "black",
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106 ## sample_point_size = 2,
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107 #if $sample_trajectory
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108 sample_trajectory = "$sample_trajectory",
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109 #if $sample_trajectory_group
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110 sample_trajectory_group = "$sample_trajectory_group",
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111 #end if
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112 #end if
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113 ## sample_plotly = NULL,
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114 #if $species_plot_cond.species_plot == "TRUE"
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115 species_plot = $species_plot_cond.species_plot,
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116 species_nlabels = $species_plot_cond.species_nlabels,
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117 species_label_taxonomy = "$species_plot_cond.species_label_taxonomy",
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118 ## species_label_size = 3,
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119 ## species_label_color = "grey10",
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120 ## species_rescale = FALSE,
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121 ## species_point_size = 2,
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122 ## species_shape = 20,
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123 ## species_plotly = FALSE,
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124 #end if
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125 #if $envfit_factor
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126 envfit_factor = "$envfit_factor",
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127 #end if
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128 #if $envfit_numeric
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129 envfit_numeric = "$envfit_numeric",
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130 #end if
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131 envfit_signif_level = $envfit_signif_level,
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132 ## envfit_textsize = 3,
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133 ## envfit_textcolor = "darkred",
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134 ## envfit_numeric_arrows_scale = 1,
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135 ## envfit_arrowcolor = "darkred",
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136 ## envfit_show = TRUE,
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137 repel_labels = $repel_labels,
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138 opacity = $opacity,
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139 tax_empty = "$tax_empty",
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140 detailed_output = TRUE,
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141 ## num_threads = 1L,
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142 )
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143 plot <- details\$plot
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144 @OUTPUT_TOKEN@
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145 ggsave("$screeplot", print(details\$screeplot), device="$output_options.out_format")
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146 ## TODO output more from model
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147 ## $model
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148 ## $dsites
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149 ## $dspecies
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150 ## $evf_factor_model
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151 ## $evf_numeric_modei
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152 ## #else
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153 ## write.table(raw, file = "$plot_raw", sep = "\t")
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154 ## #end if
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155 ]]></configfile>
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156 </configfiles>
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157 <inputs>
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158 <expand macro="rds_metadata_input_macro"/>
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159 <param argument="filter_species" type="float" value="0.1" min="0" optional="true" label="Abundance threshold" help="Remove low abundant OTU's across all samples below this threshold in percent. Setting this to 0 may drastically increase computation time."/>
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160 <conditional name="type_cond">
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161 <param argument="type" type="select" label="Ordination method" help="Note that PCoA is not performed by the vegan package, but the pcoa function from the APE package.">
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162 <option value="PCA">(PCA) Principal Components Analysis</option>
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163 <option value="RDA">(RDA) Redundancy Analysis (considered the constrained version of PCA)</option>
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164 <option value="CA">(CC) Correspondence Analysis</option>
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165 <option value="CCA">(CCA) Canonical Correspondence Analysis (considered the constrained version of CA)</option>
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166 <option value="DCA">(DCA) Detrended Correspondence Analysis</option>
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167 <option value="NMDS">(NMDS) non-metric Multidimensional Scaling</option>
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168 <option value="MMDS">(MMDS) metric Multidimensional Scaling a.k.a Principal Coordinates Analysis (not to be confused with PCA)</option>
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169 </param>
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170 <when value="PCA">
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171 <expand macro="transform_macro_hellinger"/>
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172 </when>
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173 <when value="RDA">
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174 <expand macro="transform_macro_hellinger"/>
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175 <expand macro="constrain_macro"/>
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176 </when>
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177 <when value="CA">
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178 <expand macro="transform_macro_hellinger"/>
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179 </when>
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180 <when value="CCA">
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181 <expand macro="transform_macro_hellinger"/>
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182 <expand macro="constrain_macro"/>
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183 </when>
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184 <when value="DCA">
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185 <expand macro="transform_macro_hellinger"/>
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186 </when>
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187 <when value="NMDS">
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188 <expand macro="distmeasure_macro"/>
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189 <expand macro="transform_macro">
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190 <option value="none" selected="true">No transformation</option>
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191 </expand>
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192 </when>
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193 <when value="MMDS">
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194 <expand macro="distmeasure_macro"/>
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195 <expand macro="transform_macro">
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196 <option value="none" selected="true">No transformation</option>
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197 </expand>
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198 </when>
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199 </conditional>
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200 <param argument="print_caption" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Auto-generate a figure caption" help="Based on the used arguments. The caption includes a description of how the result has been generated as well as references for the methods used."/>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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201 <expand macro="metadata_select" argument="sample_color_by" label="Color sample points by"/>
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202 <expand macro="metadata_select_discrete" argument="sample_shape_by" label="Shape sample points by"/>
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203 <expand macro="metadata_select_discrete" argument="sample_colorframe" label="Frame the sample points with a polygon by" help="Split by the variable defined by sample_color_by"/>
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204 <expand macro="metadata_select" argument="sample_colorframe_label" label="Label Frame by"/>
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205 <expand macro="metadata_select" argument="sample_label_by" label="Label sample points by"/>
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206 <expand macro="metadata_select" argument="sample_trajectory" label="Make a trajectory between sample points by"/>
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207 <expand macro="metadata_select" argument="sample_trajectory_group" label="Make a trajectory between sample points by the sample_trajectory argument, but within individual groups."/>
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208
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209 <conditional name="species_plot_cond">
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210 <param argument="species_plot" type="select" label="Plot species points">
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211 <option value="TRUE">Yes</option>
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212 <option value="FALSE" selected="true">No</option>
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213 </param>
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214 <when value="TRUE">
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215 <param argument="species_nlabels" type="integer" value="10" min="1" label="Number of the most extreme species labels to plot" help="Ordered by the sum of the numerical values of the x,y coordinates. Only makes sense with PCA/RDA)."/>
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216 <expand macro="taxlevel_macro" argument="species_label_taxonomy" label="Taxonomic level by which to label the species points">
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217 <option value="Genus" selected="true">Genus</option>
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218 </expand>
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219 <param argument="species_label_size" type="integer" value="3" min="1" label="Size of the species text labels"/>
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220 </when>
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221 <when value="FALSE"/>
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222 </conditional>
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223
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224 <expand macro="metadata_select_discrete" argument="envfit_factor" label="Categorical variables to fit onto the ordination plot"/>
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225 <expand macro="metadata_select_numeric" argument="envfit_numeric" label="Numerical variables to fit arrows onto the ordination plot." help="The lengths of the arrows are scaled by significance. "/>
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226 <param argument="envfit_signif_level" type="float" value="0.005" min="0" max="1" label="Significance threshold" help="For displaying the fitting results"/>
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227
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228 <param argument="repel_labels" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Repel all labels" help="To prevent cluttering of the plot"/>
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229 <param argument="opacity" type="float" value="0.8" min="0" max="1" label="Opacity of plotted points and colorframe" help="0: invisible, 1: opaque."/>
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230 <expand macro="tax_empty_macro"/>
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231 <expand macro="out_format_macro"/>
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232 <param name="output_screeplot" type="boolean" checked="false" label="Output screeplot" help="plot of variances against the number of the principal component"/>
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233 </inputs>
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234 <outputs>
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235 <expand macro="out_macro"/>
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236 <expand macro="out_macro" name="screeplot" label=": screeplot">
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237 <filter>output_screeplot</filter>
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238 </expand>
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239 </outputs>
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240 <tests>
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241 <!-- defaults (PCA) -->
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242 <test expect_num_outputs="2">
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243 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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244 <param name="output_screeplot" value="true"/>
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245 <output name="plot" value="AalborgWWTPs-ordinate.pdf" ftype="pdf" compare="sim_size"/>
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246 <output name="screeplot" value="AalborgWWTPs-ordinate-screeplot.pdf" ftype="pdf" compare="sim_size"/>
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247 </test>
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248 <!-- RDA + caption -->
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249 <test expect_num_outputs="1">
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250 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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251 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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252 <conditional name="type_cond">
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253 <param name="type" value="RDA"/>
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254 <param name="distmeasure" value="manhattan"/>
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255 <param name="transform" value="chi.square"/>
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256 <param name="constrain" value="Plant"/>
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257 </conditional>
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258 <output name="plot" value="AalborgWWTPs-ordinate-rda.pdf" ftype="pdf" compare="sim_size"/>
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259 </test>
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260 <!-- MMDS + unfirac (which requires a tree) -->
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261 <test expect_num_outputs="1">
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262 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
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263 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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264 <conditional name="type_cond">
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265 <param name="type" value="MMDS"/>
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266 <param name="distmeasure" value="unifrac"/>
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267 </conditional>
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268 <output name="plot" value="AalborgWWTPs-ordinate-nmds.pdf" ftype="pdf" compare="sim_size"/>
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269 </test>
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270 <!-- color, shape and colorframe -->
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271 <test expect_num_outputs="1">
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272 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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273 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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274 <param name="sample_color_by" value="Year"/>
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275 <param name="sample_shape_by" value="Plant"/>
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276 <param name="sample_colorframe" value="Year"/>
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277 <param name="sample_colorframe_label" value="Year"/>
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278 <output name="plot" value="AalborgWWTPs-ordinate-color-shape-frame.pdf" ftype="pdf" compare="sim_size"/>
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279 </test>
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280 <!-- label, trajectory -->
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281 <test expect_num_outputs="1">
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282 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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283 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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284 <param name="sample_label_by" value="Plant"/>
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285 <param name="sample_trajectory" value="Year"/>
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286 <output name="plot" value="AalborgWWTPs-ordinate-label-traj.pdf" ftype="pdf" compare="sim_size"/>
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287 </test>
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288 <!-- trajectory group -->
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289 <test expect_num_outputs="1">
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290 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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291 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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292 <param name="sample_trajectory_group" value="Plant"/>
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293 <output name="plot" value="AalborgWWTPs-ordinate-label-traj-group.pdf" ftype="pdf" compare="sim_size"/>
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294 </test>
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295 <!-- species plot -->
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296 <test expect_num_outputs="1">
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297 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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298 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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299 <conditional name="species_plot_cond">
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300 <param name="species_plot" value="TRUE"/>
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301 <param name="species_nlabels" value="2"/>
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302 <param name="species_label_taxonomy" value="Family"/>
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303 <param name="species_label_size" value="4"/>
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304 </conditional>
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305 <output name="plot" value="AalborgWWTPs-ordinate-species.pdf" ftype="pdf" compare="sim_size"/>
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306 </test>
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307 <!-- envfit factor-->
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308 <test expect_num_outputs="1">
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309 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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310 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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311 <param name="envfit_factor" value="Plant"/>
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312 <output name="plot" value="AalborgWWTPs-ordinate-envfit-factor.pdf" ftype="pdf" compare="sim_size"/>
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313 </test>
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314 <!-- envfit numeric-->
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315 <test expect_num_outputs="1">
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316 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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317 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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318 <param name="envfit_numeric" value="Year"/>
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319 <output name="plot" value="AalborgWWTPs-ordinate-envfit-num.pdf" ftype="pdf" compare="sim_size"/>
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320 </test>
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321 </tests>
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322 <help><![CDATA[
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323 What it does
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324 ============
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325
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326 Generate ordination plots suited for analysis and comparison of microbial communities.
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327
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328 The Galaxy tool calls the `amp_ordinate
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329 <https://kasperskytte.github.io/ampvis2/reference/amp_ordinate.html>`_ function
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330 of the ampvis2 package, which is a wrapper around the vegan package to generate
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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331 ggplot2 ordination plots.
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332
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333 Details
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334 =======
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335
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336 The ``amp_ordinate`` function is primarily based on two packages:
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337
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338 1. ``vegan`` package, which performs the actual ordination, and
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339 2. the ggplot2-package to generate the plot.
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340
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341 The function generates an ordination plot by the following process:
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342
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343 - Various input argument checks and error messages
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344 - OTU-table filtering, where low abundant OTU's across all samples are removed (if not **Abundance threshold** (``filter_species``) is set to 0)
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345 - Data transformation (if not **Transforms the abundances before ordination** (``transform``) is set to "no transformation").
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346 See details in `decostand <https://rdrr.io/cran/vegan/man/decostand.html>`_
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347 - Calculate distance matrix based on the chosen distmeasure if the chosen ordination method is PCoA/nMDS/DCA.
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348 See details in `vegdist <https://rdrr.io/cran/vegan/man/vegdist.html>`_
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349 - Perform the actual ordination and calculate the axis scores for both samples and species/OTU's
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350 - Visualise the result with ggplot2 or plotly in various ways defined by the user
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351
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352 When the chosen ordination method is an eigenanalysis-based method then the
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353 relative contribution (eigenvalue) of each axis to the total inertia in the data
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354 (sum of all eigenvalues, including those of the constrained space) is indicated
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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355 in percent at the axis titles. When one of the constrained ordination methods
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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356 (RDA and CCA) is used then a second value is furthermore shown which then
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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357 indicates the relative contribution of the particular axis to the total
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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358 constrained space only.
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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359
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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360 Input
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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361 =====
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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362
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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363 @HELP_RDS_INPUT@
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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364
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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365 @HELP_METADATA_LIST_INPUT@
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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366
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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367 Output
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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368 ======
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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369
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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370 An ordination plot in the chosen output format.
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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371 ]]></help>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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372 <expand macro="citations"/>
918c4abfacf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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373 </tool>