Mercurial > repos > iuc > qiime_summarize_taxa_through_plots

comparison summarize_taxa_through_plots.xml @ 5:62eb36dff24d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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&lt;designation&gt;.+)\.txt" directory="output/" /> 60 <discover_datasets pattern=".*_L(?P&lt;designation&gt;.+)\.txt" directory="output/" />
61 </collection> 61 </collection>