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comparison summarize_taxa_through_plots.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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-1:000000000000 0:c1bd0c560018
1 <tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="1.9.1">
2 <description>summaries and plots</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <version_command><![CDATA[
11 summarize_taxa_through_plots.py --version
12 ]]>
13 </version_command>
14
15 <command>
16 <![CDATA[
17 summarize_taxa_through_plots.py
18 -i $otu_table_fp
19 -o summarize_taxa_through_plots
20
21 #if $mapping_fp
22 -m $mapping_fp
23 #end if
24
25 #if $mapping_category
26 -c $mapping_category
27 #end if
28
29 $sort
30
31 &&
32
33 mkdir -p $area_charts_html_report.files_path
34 &&
35 cp -r summarize_taxa_through_plots/taxa_summary_plots/area_charts.html $area_charts_html_report.files_path
36 &&
37 cp -r summarize_taxa_through_plots/taxa_summary_plots/charts $area_charts_html_report.files_path
38 &&
39 cp -r summarize_taxa_through_plots/taxa_summary_plots/css $area_charts_html_report.files_path
40 &&
41 cp -r summarize_taxa_through_plots/taxa_summary_plots/js $area_charts_html_report.files_path
42 &&
43 mv $area_charts_html_report.files_path/area_charts.html $area_charts_html_report
44
45 &&
46 mkdir -p $bar_charts_html_report.files_path
47 &&
48 cp -r summarize_taxa_through_plots/taxa_summary_plots/bar_charts.html $bar_charts_html_report.files_path
49 &&
50 cp -r summarize_taxa_through_plots/taxa_summary_plots/charts $bar_charts_html_report.files_path
51 &&
52 cp -r summarize_taxa_through_plots/taxa_summary_plots/css $bar_charts_html_report.files_path
53 &&
54 cp -r summarize_taxa_through_plots/taxa_summary_plots/js $bar_charts_html_report.files_path
55 &&
56 mv $bar_charts_html_report.files_path/bar_charts.html $bar_charts_html_report
57
58 ]]>
59 </command>
60
61 <inputs>
62 <param name="otu_table_fp" type="data" format="biom,tabular,txt,tsv"
63 label="Input OTU table" help="(-i/--otu_table_fp)"/>
64
65 <param name="mapping_fp" type="data" format="tabular,tsv,csv"
66 label="Input metadata mapping (optional)" help="(-m, --mapping_fp)"
67 optional="True"/>
68
69 <param name="mapping_category" type="text" value="" label="Category to
70 use to summarize OTU table" help="(-c/--mapping_category)"
71 optional="True"/>
72
73 <param name="sort" type="boolean" label="Sort OTU table?"
74 truevalue="--sort" falsevalue="" selected="False"
75 help="(-s/--sort)" />
76 </inputs>
77
78 <outputs>
79 <data name="L2_tab" format="tabular"
80 from_work_dir="summarize_taxa_through_plots/*_L2.txt"
81 label="${tool.name} on ${on_string}: L2 tab">
82 <filter>"2" in level and suppress_classic_table_output is False</filter>
83 </data>
84
85 <data name="L3_tab" format="tabular"
86 from_work_dir="summarize_taxa_through_plots/*_L3.txt"
87 label="${tool.name} on ${on_string}: L3 tab">
88 <filter>"3" in level and suppress_classic_table_output is False</filter>
89 </data>
90
91 <data name="L4_tab" format="tabular"
92 from_work_dir="summarize_taxa_through_plots/*_L4.txt"
93 label="${tool.name} on ${on_string}: L4 tab">
94 <filter>"4" in level and suppress_classic_table_output is False</filter>
95 </data>
96
97 <data name="L5_tab" format="tabular"
98 from_work_dir="summarize_taxa_through_plots/*_L5.txt"
99 label="${tool.name} on ${on_string}: L5 tab">
100 <filter>"5" in level and suppress_classic_table_output is False</filter>
101 </data>
102
103 <data name="L6_tab" format="tabular"
104 from_work_dir="summarize_taxa_through_plots/*_L6.txt"
105 label="${tool.name} on ${on_string}: L6 tab">
106 <filter>"6" in level and suppress_classic_table_output is False</filter>
107 </data>
108
109 <data name="bar_charts_html_report" format="html"
110 label="${tool.name} on ${on_string}: Bar charts">
111 <filter>'bar' is chart_type</filter>
112 </data>
113
114 <data name="area_charts_html_report" format="html"
115 label="${tool.name} on ${on_string}: Area charts">
116 <filter>'area' is chart_type</filter>
117 </data>
118 </outputs>
119
120 <tests>
121 <test>
122 </test>
123 </tests>
124
125 <help><![CDATA[
126 **What it does**
127
128 This tool summarizes OTU by Category (optional), summarizes taxonomy and plots
129 taxonomy summary.
130
131 More information about this tool is available on
132 `QIIME documentation <http://qiime.org/scripts/summarize_taxa_through_plots.html>`_.
133 ]]>
134 </help>
135
136 <citations>
137 <expand macro="citations" />
138 </citations>
139
140 </tool>