Mercurial > repos > iuc > qiime_beta_diversity_through_plots

comparison beta_diversity_through_plots.xml @ 5:2140c12755d0 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 07:17:55 -0400
parents e5b102db53fd
children 70c4237c3a00
comparison
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4:10810958c6b7 5:2140c12755d0
1 <tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices and generate PCoA plots" version="@WRAPPER_VERSION@.0">
2 <description>and generate PCoA plots</description> 2 <description>(beta_diversity_through_plots)</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 <stdio> 7 <stdio>
8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/> 8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
9 </stdio> 9 </stdio>
10 <version_command>beta_diversity_through_plots.py --version</version_command> 10 <version_command>beta_diversity_through_plots.py --version</version_command>
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 beta_diversity_through_plots.py 12 beta_diversity_through_plots.py
13 --otu_table_fp '$otu_table_fp' 13 --otu_table_fp '$otu_table_fp'
14 --mapping_fp '$mapping_fp' 14 --mapping_fp '$mapping_fp'
15 --output_dir beta_diversity_through_plots 15 --output_dir beta_diversity_through_plots
16 #if $tree_fp 16 #if $tree_fp
17 --tree_fp '$tree_fp' 17 --tree_fp '$tree_fp'
18 #end if 18 #end if
19 #if $parameter_fp 19 #if $parameter_fp
20 --parameter_fp '$parameter_fp' 20 --parameter_fp '$parameter_fp'
21 #end if 21 #end if
22 $color_by_all_fields 22 $color_by_all_fields
23 $parallel 23 $parallel
24 -O "\${GALAXY_SLOTS:-4}" 24 -O "\${GALAXY_SLOTS:-4}"
25 #if $seqs_per_sample 25 #if $seqs_per_sample
26 --seqs_per_sample '$seqs_per_sample' 26 --seqs_per_sample '$seqs_per_sample'
27 #end if 27 #end if
28 $suppress_emperor_plots 28 $suppress_emperor_plots
29 29
30 && python $__tool_directory__/beta_diversity_through_plots_html_generation.py 30 && python $__tool_directory__/beta_diversity_through_plots_html_generation.py
31 --data_directory beta_diversity_through_plots 31 --data_directory beta_diversity_through_plots
32 --html_file '$beta_diversity_pcoa' 32 --html_file '$beta_diversity_pcoa'
33 --html_dir '$beta_diversity_pcoa.files_path' 33 --html_dir '$beta_diversity_pcoa.files_path'
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="True" label="OTU table"/> 36 <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="true" label="OTU table"/>
37 <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="True" label="Mapping file" help=""/> 37 <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="true" label="Mapping file"/>
38 <param argument="--tree_fp" type="data" format="txt" optional="True" label="Tree file (Optional)" help=""/> 38 <param argument="--tree_fp" type="data" format="txt" optional="true" label="Tree file (Optional)"/>
39 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/> 39 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
40 <param argument="--color_by_all_fields" type="text" optional="True" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/> 40 <param argument="--color_by_all_fields" type="text" optional="true" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/>
41 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?" help=""/> 41 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="Run in parallel where available?"/>
42 <param argument="--seqs_per_sample" type="integer" optional="True" label="Depth of coverage for even sampling (Optional)" help=""/> 42 <param argument="--seqs_per_sample" type="integer" optional="true" label="Depth of coverage for even sampling (Optional)"/>
43 <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="True" label="Generate emperor plots?" help=""/> 43 <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="true" label="Generate emperor plots?" help=""/>
44 </inputs> 44 </inputs>
45 <outputs> 45 <outputs>
46 <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics"> 46 <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics">
47 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/> 47 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/>
48 </collection> 48 </collection>