Mercurial > repos > iuc > qiime_summarize_taxa_through_plots
comparison summarize_taxa_through_plots.xml @ 5:62eb36dff24d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
---|---|
date | Sat, 05 Aug 2017 07:16:33 -0400 |
parents | 72b02cea4123 |
children | 834ef917138f |
comparison
equal
deleted
inserted
replaced
4:edd4e009d866 | 5:62eb36dff24d |
---|---|
1 <tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="@WRAPPER_VERSION@.0"> | 1 <tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy summaries and plots" version="@WRAPPER_VERSION@.0"> |
2 <description>summaries and plots</description> | 2 <description>(summarize_taxa_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 <version_command>summarize_taxa_through_plots.py --version</version_command> | 7 <version_command>summarize_taxa_through_plots.py --version</version_command> |
8 <command detect_errors="aggressive"><![CDATA[ | 8 <command detect_errors="aggressive"><![CDATA[ |
9 ## set matplotlib backend | 9 ## set matplotlib backend |
10 export MPLBACKEND="Agg" && | 10 export MPLBACKEND="Agg" && |
11 echo "backend:agg" > matplotlibrc && | 11 echo "backend:agg" > matplotlibrc && |
12 | 12 |
13 summarize_taxa_through_plots.py | 13 summarize_taxa_through_plots.py |
14 --otu_table_fp '$otu_table_fp' | 14 --otu_table_fp '$otu_table_fp' |
15 --output_dir output | 15 --output_dir output |
16 #if $parameter_fp | 16 #if $parameter_fp |
17 --parameter_fp '$parameter_fp' | 17 --parameter_fp '$parameter_fp' |
18 #end if | 18 #end if |
19 #if $mapping.use_mapping == "yes" | 19 #if $mapping.use_mapping == "yes" |
20 --mapping_fp '$mapping.mapping_fp' | 20 --mapping_fp '$mapping.mapping_fp' |
21 #if str($mapping.mapping_category) != '' | 21 #if str($mapping.mapping_category) != '' |
22 --mapping_category '$mapping.mapping_category' | 22 --mapping_category '$mapping.mapping_category' |
23 #end if | 23 #end if |
24 #end if | 24 #end if |
25 $sort | 25 $sort |
26 && mkdir -p '$area_charts_html_report.files_path' | 26 && mkdir -p '$area_charts_html_report.files_path' |
27 && cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path' | 27 && cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path' |
28 && cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path' | 28 && cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path' |
29 && cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path' | 29 && cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path' |
30 && cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path' | 30 && cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path' |
31 && cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path' | 31 && cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path' |
32 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' | 32 && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report' |
33 | 33 |
34 && mkdir -p '$bar_charts_html_report.files_path' | 34 && mkdir -p '$bar_charts_html_report.files_path' |
35 && cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path' | 35 && cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path' |
36 && cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path' | 36 && cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path' |
37 && cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path' | 37 && cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path' |
38 && cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path' | 38 && cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path' |
39 && cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path' | 39 && cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path' |
40 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' | 40 && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report' |
41 ]]></command> | 41 ]]></command> |
42 <inputs> | 42 <inputs> |
43 <param argument="--otu_table_fp" type="data" format="biom1,tabular,txt" label="Input OTU table"/> | 43 <param argument="--otu_table_fp" type="data" format="biom1,tabular,txt" label="Input OTU table"/> |
44 <conditional name="mapping"> | 44 <conditional name="mapping"> |
45 <param name="use_mapping" type="select" label="Use a metadata mapping file?"> | 45 <param name="use_mapping" type="select" label="Use a metadata mapping file?"> |
46 <option value="yes">Yes</option> | 46 <option value="yes">Yes</option> |
47 <option value="no">No</option> | 47 <option value="no">No</option> |
48 </param> | 48 </param> |
49 <when value="yes"> | 49 <when value="yes"> |
50 <param argument="--mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping"/> | 50 <param argument="--mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping"/> |
51 <param argument="--mapping_category" type="text" value="" label="Category to use to summarize OTU table" optional="True"/> | 51 <param argument="--mapping_category" type="text" value="" optional="true" label="Category to use to summarize OTU table"/> |
52 </when> | 52 </when> |
53 <when value="no"/> | 53 <when value="no"/> |
54 </conditional> | 54 </conditional> |
55 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/> | 55 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends"/> |
56 <param argument="--sort" type="boolean" label="Sort OTU table?" truevalue="--sort" falsevalue="" checked="False"/> | 56 <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="" checked="false" label="Sort OTU table?"/> |
57 </inputs> | 57 </inputs> |
58 <outputs> | 58 <outputs> |
59 <collection name="otu_table" type="list" label="${tool.name} on ${on_string}: OTU tables for the different taxonomic levels"> | 59 <collection name="otu_table" type="list" label="${tool.name} on ${on_string}: OTU tables for the different taxonomic levels"> |
60 <discover_datasets pattern=".*_L(?P<designation>.+)\.txt" directory="output/" /> | 60 <discover_datasets pattern=".*_L(?P<designation>.+)\.txt" directory="output/" /> |
61 </collection> | 61 </collection> |