Mercurial > repos > iuc > qiime_summarize_taxa

comparison summarize_taxa.xml @ 0:2f2e4388bd05 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:30:59 -0400
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children 50df54a9ae82
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-1:000000000000 0:2f2e4388bd05
1 <tool id="qiime_summarize_taxa" name="Summarize taxa" version="@WRAPPER_VERSION@.0">
2 <description>and store results in a new table or appended to an existing mapping file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>summarize_taxa.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 summarize_taxa.py
10 -i '$otu_table_fp'
11 -o summarize_taxa
12 -L '$level'
13 #if str($mapping) != 'None':
14 -m '$mapping'
15 #end if
16 --md_identifier $md_identifier
17 $md_as_string
18 $absolute_abundance
19 #if str( $lower_percentage )
20 -l '$lower_percentage'
21 #end if
22 #if str( $upper_percentage)
23 -u '$upper_percentage'
24 #end if
25 $transposed_output
26 $suppress_classic_table_output
27 $suppress_biom_table_output
28 ]]></command>
29 <inputs>
30 <param argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table" help="(-i/)"/>
31 <param argument="--level" type="select" label="Taxonomic level to summarize by" multiple="True" display="checkboxes">
32 <option value="1">Kingdom</option>
33 <option value="2" selected="true">Phylum</option>
34 <option value="3" selected="true">Class</option>
35 <option value="4" selected="true">Order</option>
36 <option value="5" selected="true">Family</option>
37 <option value="6" selected="true">Genus</option>
38 <option value="7">Species</option>
39 </param>
40 <param argument="--mapping" type="data" format="tabular,tsv,csv" label="Input metadata mapping (optional)" help="If supplied, then the taxon information will be added to this file. This option is useful for coloring PCoA plots by taxon abundance or to perform statistical tests of taxon/mapping associations" optional="True"/>
41 <param argument="--md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key"/>
42 <param argument="--md_as_string" type="boolean" label="Include metadata as string?" truevalue="--md_as_string" falsevalue="" checked="False" help="By default, metadata is included as list"/>
43 <param argument="--absolute_abundance" type="boolean" label="Report absolute abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False" help="By default, relative abundance is reported"/>
44 <param argument="lower_percentage" type="float" label="Percentage threshold to remove highly present OTU (optional)" help="If present, OTUs having higher absolute abundance are trimmed. To remove OTUs that make up more than 5% of the total dataset you would pass 0.05" optional="True"/>
45 <param argument="--upper_percentage" type="float" label="Percentage threshold to remove lowly present OTU (optional)" help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45" optional="True"/>
46 <param argument="--transposed_output" type="boolean" label="Transpose output?" truevalue="--transposed_output" falsevalue="" checked="False" help="If checked, the output will be written transposed from the regular output. This is helpful in cases when you want to use Site Painter to visualize your data"/>
47 <param argument="--suppress_classic_table_output" type="boolean" label="Suppress creation of the classic (TSV) format taxon table?" truevalue="--suppress_classic_table_output" falsevalue="" checked="False" help="This option is ignored if a mapping file is present"/>
48 <param argument="--suppress_biom_table_output" type="boolean" label="Suppress creation of the BIOM-formatted taxon table?" truevalue="--suppress_biom_table_output" falsevalue="" checked="False" help="This option is ignored if a mapping file is present"/>
49 </inputs>
50 <outputs>
51 <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" label="${tool.name} on ${on_string}: L1 tab">
52 <filter>"1" in level and suppress_classic_table_output is False</filter>
53 </data>
54 <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab">
55 <filter>"2" in level and suppress_classic_table_output is False</filter>
56 </data>
57 <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab">
58 <filter>"3" in level and suppress_classic_table_output is False</filter>
59 </data>
60 <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab">
61 <filter>"4" in level and suppress_classic_table_output is False</filter>
62 </data>
63 <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab">
64 <filter>"5" in level and suppress_classic_table_output is False</filter>
65 </data>
66 <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab">
67 <filter>"6" in level and suppress_classic_table_output is False</filter>
68 </data>
69 <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" label="${tool.name} on ${on_string}: L7 tab">
70 <filter>"7" in level and suppress_classic_table_output is False</filter>
71 </data>
72 </outputs>
73 <tests>
74 <test>
75 <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>
76 <param name="level" value="2,3,4,5,6"/>
77 <param name="mapping" value="summarize_taxa/map.txt"/>
78 <param name="md_identifier" value="taxonomy"/>
79 <param name="md_as_string" value=""/>
80 <param name="absolute_abundance" value=""/>
81 <param name="transposed_output" value=""/>
82 <param name="suppress_classic_table_output" value=""/>
83 <param name="suppress_biom_table_output" value=""/>
84 <output name="L2_tab" value="summarize_taxa/1_L2.txt"/>
85 <output name="L3_tab" value="summarize_taxa/1_L3.txt"/>
86 <output name="L4_tab" value="summarize_taxa/1_L4.txt"/>
87 <output name="L5_tab" value="summarize_taxa/1_L5.txt"/>
88 <output name="L6_tab" value="summarize_taxa/1_L6.txt"/>
89 </test>
90 <test>
91 <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>
92 <param name="level" value="3,6"/>
93 <param name="md_identifier" value="taxonomy"/>
94 <param name="md_as_string" value=""/>
95 <param name="absolute_abundance" value=""/>
96 <param name="transposed_output" value=""/>
97 <param name="suppress_classic_table_output" value=""/>
98 <param name="suppress_biom_table_output" value=""/>
99 <output name="L3_tab" value="summarize_taxa/2_L3.txt"/>
100 <output name="L6_tab" value="summarize_taxa/2_L6.txt"/>
101 </test>
102 </tests>
103 <help><![CDATA[
104 **What it does**
105
106 This tool provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input.
107
108 More information about this tool is available on
109 `QIIME documentation <http://qiime.org/scripts/summarize_taxa.html>`_.
110 ]]></help>
111 <citations>
112 <expand macro="citations"/>
113 </citations>
114 </tool>