Mercurial > repos > iuc > qiime_alpha_diversity

comparison alpha_diversity.xml @ 5:ffe438e1fc67 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:26:40 -0400
parents 2ceee245d97c
children 1fa3942bec04
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4:f6e1b1b9b2dd 5:ffe438e1fc67
1 <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0">
2 <description>on each sample in an otu table</description> 2 <description> on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>alpha_diversity.py --version</version_command> 7 <version_command>alpha_diversity.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 #set $chosen_metrics = str( $metrics ).split( "," ) 9 #set $chosen_metrics = str( $metrics ).split( "," )
10 alpha_diversity.py 10 alpha_diversity.py
11 --input_path '$input_path' 11 --input_path '$input_path'
12 -o alphadiv 12 -o alphadiv
13 --metrics '$metrics' 13 --metrics '$metrics'
14 #if "PD_whole_tree" in $chosen_metrics: 14 #if "PD_whole_tree" in $chosen_metrics:
15 --tree_path '$tree_path' 15 --tree_path '$tree_path'
16 #end if 16 #end if
17 ]]></command> 17 ]]></command>
18 <inputs> 18 <inputs>
19 <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True" label="OTU table"/> 19 <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True" label="OTU table"/>
20 <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use"> 20 <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use">
21 <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option> 21 <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
22 <option value="berger_parker_d">Berger-Parker dominance</option> 22 <option value="berger_parker_d">Berger-Parker dominance</option>
23 <option value="brillouin_d">Brillouin index of alpha diversity</option> 23 <option value="brillouin_d">Brillouin index of alpha diversity</option>
24 <option value="chao1" selected="true">chao1 richness estimator</option> 24 <option value="chao1" selected="true">chao1 richness estimator</option>
25 <option value="chao1_ci">chao1 confidence interval</option> 25 <option value="chao1_ci">chao1 confidence interval</option>
48 <option value="simpson_e">Simpson’s evenness measure E</option> 48 <option value="simpson_e">Simpson’s evenness measure E</option>
49 <option value="singles">Number of single occurrencesles</option> 49 <option value="singles">Number of single occurrencesles</option>
50 <option value="strong"> Strong’s dominance index</option> 50 <option value="strong"> Strong’s dominance index</option>
51 <option value="PD_whole_tree">Phylogenetic diversity</option> 51 <option value="PD_whole_tree">Phylogenetic diversity</option>
52 </param> 52 </param>
53 <param argument="--tree_path" type="data" format="nhx" optional="True" label="Newick tree (optional, except for PD_whole_tree metric)"/> 53 <param argument="--tree_path" type="data" format="nhx" optional="true" label="Newick tree (optional, except for PD_whole_tree metric)"/>
54 </inputs> 54 </inputs>
55 <outputs> 55 <outputs>
56 <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/> 56 <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/>
57 </outputs> 57 </outputs>
58 <tests> 58 <tests>