Mercurial > repos > iuc > vegan_rarefaction

comparison vegan_rarefaction.xml @ 3:af1211ed6c8e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit f93edebf6c946402f105f0622aacb0baa216a70c
author iuc
date Fri, 15 Mar 2024 15:26:48 +0000
parents b0d5976540e3
children
comparison
equal deleted inserted replaced
2:b0d5976540e3 3:af1211ed6c8e
3 curve and statistics 3 curve and statistics
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="bio.tools_xrefs" />
8 <expand macro="requirements" /> 9 <expand macro="requirements" />
9 <expand macro="stdio" /> 10 <expand macro="stdio" />
10 <expand macro="version_command" /> 11 <expand macro="version_command" />
11 <command><![CDATA[ 12 <command><![CDATA[
12 #if "output_r_script" in str( $include_outputs ).split( "," ): 13 #if "output_r_script" in str( $include_outputs ).split( "," ):
107 <data format="txt" name="output_r_script" label="${tool.name} on ${on_string} (Rscript)"> 108 <data format="txt" name="output_r_script" label="${tool.name} on ${on_string} (Rscript)">
108 <filter>"output_r_script" in include_outputs</filter> 109 <filter>"output_r_script" in include_outputs</filter>
109 </data> 110 </data>
110 </outputs> 111 </outputs>
111 <tests> 112 <tests>
112 <test> 113 <test expect_num_outputs="7">
113 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/> 114 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
114 <param name="species_column" value="6"/> 115 <param name="species_column" value="6"/>
115 <param name="sample_columns" value="2"/> 116 <param name="sample_columns" value="2"/>
116 <param name="sample_size" value=""/> 117 <param name="sample_size" value=""/>
117 <param name="step_size" value="1"/> 118 <param name="step_size" value="1"/>
121 <output name="output_species_count" ftype="tabular" file="vegan_output_species_count.tabular" /> 122 <output name="output_species_count" ftype="tabular" file="vegan_output_species_count.tabular" />
122 <output name="output_species_frequency" ftype="tabular" file="vegan_output_species_frequency.tabular" /> 123 <output name="output_species_frequency" ftype="tabular" file="vegan_output_species_frequency.tabular" />
123 <output name="output_richness" ftype="tabular" file="vegan_output_richness.tabular" /> 124 <output name="output_richness" ftype="tabular" file="vegan_output_richness.tabular" />
124 <output name="output_species_probabilities" ftype="tabular" file="vegan_output_species_probabilities.tabular" /> 125 <output name="output_species_probabilities" ftype="tabular" file="vegan_output_species_probabilities.tabular" />
125 <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" /> 126 <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" />
127 <output name="output_plot" ftype="png" file="vegan_output_plot.png" compare="sim_size" />
128 <output name="output_random_rarefied" ftype="tabular" file="vegan_output_random_rarefied.tabular" />
126 </test> 129 </test>
127 </tests> 130 </tests>
128 <help> 131 <help>
129 <![CDATA[ 132 <![CDATA[
130 133
138 .. class:: warningmark 141 .. class:: warningmark
139 142
140 When subsampling by community size, slope of the rarefaction curve and species probabilities are computed using community size-1 143 When subsampling by community size, slope of the rarefaction curve and species probabilities are computed using community size-1
141 ]]> 144 ]]>
142 </help> 145 </help>
143 <citations> 146 <expand macro="citations" />
144 </citations>
145 </tool> 147 </tool>