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comparison summarize_taxa.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 <tool id="qiime_summarize_taxa" name="Summarize taxa" version="1.9.1">
2 <description>and store results in a new table or appended to an existing
3 mapping file
4 </description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements" />
11
12 <version_command><![CDATA[
13 summarize_taxa.py --version
14 ]]>
15 </version_command>
16
17 <command>
18 <![CDATA[
19 summarize_taxa.py
20 -i $otu_table_fp
21 -o summarize_taxa
22
23 -L $level
24
25 #if str($mapping) != 'None':
26 -m $mapping
27 #end if
28
29 --md_identifier $md_identifier
30
31 $md_as_string
32
33 $absolute_abundance
34
35 #if str( $lower_percentage )
36 -l $lower_percentage
37 #end if
38
39 #if str( $upper_percentage)
40 -u $upper_percentage
41 #end if
42
43 $transposed_output
44 $suppress_classic_table_output
45 $suppress_biom_table_output
46 ]]>
47 </command>
48
49 <inputs>
50 <param name="otu_table_fp" type="data" format="tabular,tsv,txt,biom"
51 label="Input OTU table" help="(-i/--otu_table_fp)"/>
52
53 <param name="level" type="select" label="Taxonomic level to summarize by"
54 help="(-L/--level)" multiple="True" display="checkboxes">
55 <option value="1" >Kingdom</option>
56 <option value="2" selected="true">Phylum</option>
57 <option value="3" selected="true">Class</option>
58 <option value="4" selected="true">Order</option>
59 <option value="5" selected="true">Family</option>
60 <option value="6" selected="true">Genus</option>
61 <option value="7" >Species</option>
62 </param>
63
64 <param name="mapping" type="data" format="tabular,tsv,csv"
65 label="Input metadata mapping (optional)" help="If supplied, then the
66 taxon information will be added to this file. This option is useful for
67 coloring PCoA plots by taxon abundance or to perform statistical
68 tests of taxon/mapping associations (-m/--mapping)" optional="True"/>
69
70 <param name="md_identifier" type="text" value="taxonomy" label="Relevant
71 observation metadata key" help="(--md_identifier)" />
72
73 <param name="md_as_string" type="boolean" label="Include metadata as string?"
74 truevalue="--md_as_string" falsevalue="" checked="False"
75 help="By default, metadata is included as list (--md_as_string)" />
76
77 <param name="absolute_abundance" type="boolean" label="Report absolute
78 abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False"
79 help="By default, relative abundance is reported (--absolute_abundance)" />
80
81 <param name="lower_percentage" type="float" label="Percentage threshold to
82 remove highly present OTU (optional)" help="If present, OTUs having
83 higher absolute abundance are trimmed. To remove OTUs that make up
84 more than 5% of the total dataset you would pass 0.05 (-l/--lower_percentage)"
85 optional="True"/>
86
87 <param name="upper_percentage" type="float" label="Percentage threshold to
88 remove lowly present OTU (optional)" help="If present, OTUs having
89 lower absolute abundance are trimmed. To remove the OTUs that
90 makes up less than 45% of the total dataset you would pass 0.45
91 (-u/--upper_percentage)" optional="True"/>
92
93 <param name="transposed_output" type="boolean" label="Transpose output?"
94 truevalue="--transposed_output" falsevalue="" checked="False"
95 help="If checked, the output will be written transposed from the
96 regular output. This is helpful in cases when you want to use Site
97 Painter to visualize your data (-t/--transposed_output)" />
98
99 <param name="suppress_classic_table_output" type="boolean"
100 label="Suppress creation of the classic (TSV) format taxon table?"
101 truevalue="--suppress_classic_table_output" falsevalue="" checked="False"
102 help="This option is ignored if a mapping file is present
103 (--suppress_classic_table_output)" />
104
105 <param name="suppress_biom_table_output" type="boolean"
106 label="Suppress creation of the BIOM-formatted taxon table?"
107 truevalue="--suppress_biom_table_output" falsevalue="" checked="False"
108 help="This option is ignored if a mapping file is present
109 (--suppress_biom_table_output)" />
110 </inputs>
111
112 <outputs>
113 <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt"
114 label="${tool.name} on ${on_string}: L1 tab">
115 <filter>"1" in level and suppress_classic_table_output is False</filter>
116 </data>
117
118 <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt"
119 label="${tool.name} on ${on_string}: L2 tab">
120 <filter>"2" in level and suppress_classic_table_output is False</filter>
121 </data>
122
123 <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt"
124 label="${tool.name} on ${on_string}: L3 tab">
125 <filter>"3" in level and suppress_classic_table_output is False</filter>
126 </data>
127
128 <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt"
129 label="${tool.name} on ${on_string}: L4 tab">
130 <filter>"4" in level and suppress_classic_table_output is False</filter>
131 </data>
132
133 <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt"
134 label="${tool.name} on ${on_string}: L5 tab">
135 <filter>"5" in level and suppress_classic_table_output is False</filter>
136 </data>
137
138 <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt"
139 label="${tool.name} on ${on_string}: L6 tab">
140 <filter>"6" in level and suppress_classic_table_output is False</filter>
141 </data>
142
143 <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt"
144 label="${tool.name} on ${on_string}: L7 tab">
145 <filter>"7" in level and suppress_classic_table_output is False</filter>
146 </data>
147 </outputs>
148
149 <tests>
150 <test>
151 <param name="otu_table_fp"
152 value="pick_open_reference_otus_otu_table_with_taxo.biom"/>
153 <param name="level" value="2,3,4,5,6" />
154 <param name="mapping"
155 value="validate_mapping_file_corrected_map.tabular"/>
156 <param name="md_identifier" value="taxonomy"/>
157 <param name="md_as_string" value=""/>
158 <param name="delimiter" value=";" />
159 <param name="absolute_abundance" value=""/>
160 <param name="transposed_output" value=""/>
161 <param name="suppress_classic_table_output" value="" />
162 <param name="suppress_biom_table_output" value="" />
163
164 <output name="L2_tab" value="summarize_taxa_L2.tabular" />
165 <output name="L3_tab" value="summarize_taxa_L3.tabular" />
166 <output name="L4_tab" value="summarize_taxa_L4.tabular" />
167 <output name="L5_tab" value="summarize_taxa_L5.tabular" />
168 <output name="L6_tab" value="summarize_taxa_L6.tabular" />
169 </test>
170 </tests>
171
172 <help><![CDATA[
173
174 **What it does**
175
176 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.
177
178 More information about this tool is available on
179 `QIIME documentation <http://qiime.org/scripts/summarize_taxa.html>`_.
180 ]]>
181 </help>
182
183 <citations>
184 <expand macro="citations" />
185 </citations>
186 </tool>