Mercurial > repos > iuc > qiime_compare_categories
comparison compare_categories.xml @ 5:21abe2afb7cf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 07:20:31 -0400 |
parents | fd2ec7008305 |
children | 951cc7b6fca6 |
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4:0bb58d2f80a3 | 5:21abe2afb7cf |
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1 <tool id="qiime_compare_categories" name="Analyzes statistical significance" version="@WRAPPER_VERSION@.0"> | 1 <tool id="qiime_compare_categories" name="Analyze statistical significance of sample groupings" version="@WRAPPER_VERSION@.0"> |
2 <description>of sample groupings using distance matrices</description> | 2 <description> using distance matrices (compare_categories)</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 <requirement type="package" version="1.3.2">r-optparse</requirement> | 7 <requirement type="package" version="1.3.2">r-optparse</requirement> |
8 <requirement type="package" version="2.3_4">r-vegan</requirement> | 8 <requirement type="package" version="2.3_4">r-vegan</requirement> |
9 <requirement type="package" version="3.3">r-base</requirement> | 9 <requirement type="package" version="3.3">r-base</requirement> |
10 </expand> | 10 </expand> |
11 <version_command>compare_categories.py --version</version_command> | 11 <version_command>compare_categories.py --version</version_command> |
12 <command detect_errors="aggressive"><![CDATA[ | 12 <command detect_errors="aggressive"><![CDATA[ |
13 compare_categories.py | 13 compare_categories.py |
14 --method '$method' | 14 --method '$method' |
15 --input_dm '$input_dm' | 15 --input_dm '$input_dm' |
16 --mapping_file '$mapping_file' | 16 --mapping_file '$mapping_file' |
17 --categories '$categories' | 17 --categories '$categories' |
18 -o compare_categories | 18 -o compare_categories |
19 #if $num_permutations | 19 #if $num_permutations |
20 --num_permutations '$num_permutations' | 20 --num_permutations '$num_permutations' |
21 #end if | 21 #end if |
22 ]]></command> | 22 ]]></command> |
23 <inputs> | 23 <inputs> |
24 <param argument="--method" label="Select the statistical method to use" type="select"> | 24 <param argument="--method" type="select" label="Select the statistical method to use"> |
25 <option value="adonis">adonis</option> | 25 <option value="adonis">adonis</option> |
26 <option value="anosim">anosim</option> | 26 <option value="anosim">anosim</option> |
27 <option value="bioenv">bioenv</option> | 27 <option value="bioenv">bioenv</option> |
28 <option value="morans_i">morans_i</option> | 28 <option value="morans_i">morans_i</option> |
29 <option value="mrpp">mrpp</option> | 29 <option value="mrpp">mrpp</option> |
32 <option value="dbrda">dbrda</option> | 32 <option value="dbrda">dbrda</option> |
33 </param> | 33 </param> |
34 <param argument="--input_dm" type="data" format="txt,tabular,tsv" label="Input distance matrix" help="Only symmetric, hollow distance matrices may be used as input. Asymmetric distance matrices, such as those obtained by the UniFrac Gain metric (i.e. beta_diversity.py -m unifrac_g), should not be used as input"/> | 34 <param argument="--input_dm" type="data" format="txt,tabular,tsv" label="Input distance matrix" help="Only symmetric, hollow distance matrices may be used as input. Asymmetric distance matrices, such as those obtained by the UniFrac Gain metric (i.e. beta_diversity.py -m unifrac_g), should not be used as input"/> |
35 <param argument="--mapping_file" type="data" format="tabular,txt,tsv" label="Mapping file"/> | 35 <param argument="--mapping_file" type="data" format="tabular,txt,tsv" label="Mapping file"/> |
36 <param argument="--categories" type="text" label="Comma-delimited list of categories from the mapping file" help="All methods except for BIO-ENV accept just a single category. If multiple categories are provided, only the first will be used"/> | 36 <param argument="--categories" type="text" label="Comma-delimited list of categories from the mapping file" help="All methods except for BIO-ENV accept just a single category. If multiple categories are provided, only the first will be used"/> |
37 <param argument="--num_permutations" type="integer" label="Number of permutations to use when calculating statistical significance" help="Only applies to adonis, ANOSIM, MRPP, PERMANOVA, PERMDISP, and db-RDA. Must be greater than or equal to zero" optional="True" value="999" min="0"/> | 37 <param argument="--num_permutations" type="integer" value="999" min="0" optional="True" label="Number of permutations to use when calculating statistical significance" help="Only applies to adonis, ANOSIM, MRPP, PERMANOVA, PERMDISP, and db-RDA. Must be greater than or equal to zero"/> |
38 </inputs> | 38 </inputs> |
39 <outputs> | 39 <outputs> |
40 <data name="test_results" format="txt" from_work_dir="compare_categories/*_results.txt" label="${tool.name} on ${on_string}: Test resuts"/> | 40 <data name="test_results" format="txt" from_work_dir="compare_categories/*_results.txt" label="${tool.name} on ${on_string}: Test resuts"/> |
41 <data name="dbrda_plot" format="pdf" from_work_dir="compare_categories/dbrda_plot.pdf" label="${tool.name} on ${on_string}: Ordination plot"> | 41 <data name="dbrda_plot" format="pdf" from_work_dir="compare_categories/dbrda_plot.pdf" label="${tool.name} on ${on_string}: Ordination plot"> |
42 <filter>(method == 'dbrda')</filter> | 42 <filter>(method == 'dbrda')</filter> |