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comparison copyrighter.xml @ 0:7a7ecf9b9df7 draft

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Initial upload
author fangly
date Mon, 29 Jul 2013 06:52:36 -0400
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-1:000000000000 0:7a7ecf9b9df7
1 <tool id="copyrighter" name="CopyRighter" version="0.45">
2
3 <description>trait bias corrector for microbial profiles</description>
4
5 <requirements>
6 <requirement type="binary">copyrighter</requirement>
7 </requirements>
8
9 <version_string>copyrighter --version</version_string>
10
11 <command>
12 copyrighter
13 -i $input
14 -d $database.value
15 #if str($lookup):
16 -l $lookup
17 #end if
18 #if str($total) != "None":
19 -t $total
20 #end if
21 #if str($verbose):
22 -v
23 #end if
24 </command>
25
26 <inputs>
27 <param name="input" type="data" format="txt" label="Input community file" help="Text file obtained from 16S rRNA microarray, 16S rRNA amplicon sequencing or metagenomic sequencing, in biom, QIIME, GAAS, Unifrac, or generic (tabular site-by-species) format. The file must contain read counts (not percentages) and taxa must have UNALTERED taxonomic assignments." />
28 <conditional name="database">
29 <param name="specify" type="select" label="Trait database" help="Tab-delimited file of traits: 16S copy number, genome length, ...">
30 <option value="builtin">Built-in file</option>
31 <option value="uploaded">Uploaded file</option>
32 </param>
33 <when value="builtin">
34 <param name="value" type="select" label="Built-in file">
35 <options from_data_table="trait_db" />
36 <validator type="no_options" message="No built-in trait database is available"/>
37 </param>
38 </when>
39 <when value="uploaded">
40 <param name="value" type="data" format="tabular" label="Uploaded file" />
41 </when>
42 </conditional>
43 <param name="lookup" type="select" display="radio" value="desc" label="Lookup method" help="What to match when looking up the trait value of a taxon.">
44 <option value="desc">OTU name</option>
45 <option value="id">OTU ID (if recorded in your input community file)</option>
46 </param>
47 <param name="total" type="data" format="tabular" optional="true" label="Total abundance file" help="Tab-delimited file containing the total microbial abundance of each community, e.g. 16S rRNA quantitative PCR numbers to be corrected by the average 16S rRNA copy number." />
48 <param name="verbose" type="boolean" checked="no" truevalue="1" falsevalue="0" format="txt" label="Verbose" help="Display trait value assignments." />
49 </inputs>
50
51 <outputs>
52 <data format="txt" name="relative" from_work_dir="out_copyrighted.txt" label="${tool.name} from ${on_string} (relative)"/>
53 <data format="tabular" name="absolute" from_work_dir="out_copyrighted_total.tsv" label="${tool.name} from ${on_string} (absolute)">
54 <filter>str(total) != "None"</filter>
55 </data>
56 <data format="txt" name="combined" from_work_dir="out_copyrighted_combined.txt" label="${tool.name} from ${on_string} (combined)">
57 <filter>str(total) != "None"</filter>
58 </data>
59 </outputs>
60
61 <stdio>
62 <exit_code range="1:" level="fatal" />
63 <regex match="error|exception|invalid" source="stderr" level="fatal" />
64 </stdio>
65
66 <tests>
67 <test>
68 <param name="input" value="test_data/in.qiime" />
69 <param name="specify" value="uploaded"/>
70 <param name="value" value="test_data/in_db.tsv"/>
71 <output name="relative" file="test_data/out.qiime"/>
72 </test>
73 <test>
74 <param name="input" value="test_data/in.biom"/>
75 <param name="specify" value="uploaded"/>
76 <param name="value" value="test_data/in_db.tsv"/>
77 <output name="relative" file="test_data/out.biom" lines_diff="2"/>
78 </test>
79 <test>
80 <param name="input" value="test_data/in.qiime"/>
81 <param name="specify" value="uploaded"/>
82 <param name="value" value="test_data/in_db.tsv"/>
83 <param name="verbose" value="yes"/>
84 <output name="relative" file="test_data/out.qiime"/>
85 </test>
86 <test>
87 <param name="input" value="test_data/in.biom"/>
88 <param name="specify" value="uploaded"/>
89 <param name="value" value="test_data/in_db.tsv"/>
90 <param name="lookup" value="id"/>
91 <output name="relative" file="test_data/out2.biom" lines_diff="2"/>
92 </test>
93 <test>
94 <param name="input" value="test_data/in.qiime"/>
95 <param name="specify" value="uploaded"/>
96 <param name="value" value="test_data/in_db.tsv"/>
97 <param name="total" value="test_data/in_total.tsv"/>
98 <output name="relative" file="test_data/out.qiime"/>
99 <output name="absolute" file="test_data/out_total.tsv"/>
100 <output name="combined" file="test_data/out_combined.qiime"/>
101 </test>
102 <!--<test>
103 <param name="input" value="test_data/in.biom"/>
104 <param name="specify" value="builtin"/>
105 <param name="value" value="test_data/in_db.tsv"/>
106 <output name="relative" file="test_data/out.biom" lines_diff="2"/>
107 </test>-->
108 </tests>
109
110 <help>
111 **What CopyRighter does**
112
113 The genome of Bacteria and Archaea often contains several copies of the
114 16S rRNA gene. This can lead to significant biases when estimating the
115 composition of microbial communities using 16S rRNA amplicons or
116 microarrays or their total abundance using 16S rRNA quantitative PCR,
117 since species with a large number of copies will contribute
118 disproportionally more 16S amplicons than species with a unique copy.
119 Fortunately, it is possible to infer the copy number of unsequenced
120 microbial species, based on that of close relatives that have been fully
121 sequenced. Using this information, CopyRigher corrects microbial
122 relative abundance by applying a weight proportional to the inverse of
123 the estimated copy number to each species.
124
125 In metagenomic surveys, a similar problem arises due to genome length
126 variations between species, and can be corrected by CopyRighter as well.
127
128 In all cases, a community file is used as input and a corrected community
129 file with trait-corrected (16S rRNA gene copy number or genome length)
130 relative abundances is generated. Total abundance can optionally be
131 provided, corrected and combined with relative abundance estimates to
132 get the absolute abundance of each species. Also the average trait value
133 in each community is reported on standard output.
134 </help>
135
136 </tool>
137