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comparison make_otu_table.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_make_otu_table" name="make otu table" version="1.9.1galaxy1">
2
3 <description>Make OTU table</description>
4
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8
9 <expand macro="requirements" />
10
11 <command>
12 <![CDATA[
13 make_otu_table.py
14 -i $otu_map_fp
15 -o $output_biom_fp
16 #if str($taxonomy) != 'None':
17 -t $taxonomy
18 #end if
19
20 #if str($exclude_otus_fp) != 'None':
21 -e $exclude_otus_fp
22 #end if
23 ]]>
24 </command>
25
26 <inputs>
27 <param label="-i/--otu_map_fp: path to the input OTU map (i.e., the output
28 from pick_otus.py)" name="otu_map_fp" optional="False" type="data"/>
29 <param label="-t/--taxonomy: Path to taxonomy assignment, containing the
30 assignments of taxons to sequences (i.e., resulting txt file from
31 assign_taxonomy.py) [default: None]" name="taxonomy" optional="True"
32 type="data"/>
33 <param label="-e/--exclude_otus_fp: path to a file listing OTU identifiers
34 that should not be included in the OTU table (e.g., the output of
35 identify_chimeric_seqs.py) or a fasta file where seq ids should be
36 excluded (e.g., failures fasta file from align_seqs.py)"
37 name="exclude_otus_fp" optional="True" type="data"/>
38 </inputs>
39
40 <outputs>
41 <data format="txt" name="output_biom_fp" label="otu_table.biom"/>
42 </outputs>
43
44 <tests>
45 <test>
46 </test>
47 </tests>
48
49 <help><![CDATA[
50
51 **What it does**
52
53 The script make_otu_table.py tabulates the number of times an OTU is found in each
54 sample, and adds the taxonomic predictions for each OTU in the last column if a
55 taxonomy file is supplied.
56 The output of make_otu_table.py is a biom file, where the columns correspond to
57 Samples and rows correspond to OTUs and the number of times a sample appears in
58 a particular OTU.
59 ]]>
60 </help>
61
62 <citations>
63 <expand macro="citations" />
64 </citations>
65 </tool>