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comparison compare_biom.xml @ 0:43244ad9e7ef draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
author iuc
date Sat, 20 Jan 2018 03:31:34 -0500
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1 <tool id="picrust_compare_biom" name="Compare BIOM tables" version="@WRAPPER_VERSION@.0">
2 <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[
9 compare_biom.py
10 -e '$expected'
11 -o '$outfile'
12 $not_relative_abundance_scores
13 $advanced.normalize
14 $advanced.limit_to_observed_observations
15 $advanced.limit_to_expected_observations
16 $advanced.shuffle_samples
17
18 '$observed'
19 ]]></command>
20 <inputs>
21 <param name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/>
22 <param name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/>
23 <param argument="not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?"
24 help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/>
25 <section name="advanced" title="Advanced parameters" expanded="false">
26 <param argument="compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations"
27 help="Calculate accuracy values by comparing between observations (instead of between samples)."/>
28 <param argument="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?"
29 help="Convert both expected and observed tables to relative abundances (instead of observations)."/>
30 <param argument="limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?"
31 help="Ignore observations that are not in the observed table."/>
32 <param argument="limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?"
33 help="Ignore observations that are not in the expected table."/>
34 <param argument="shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?"
35 help="Shuffle samples ids randomly before measuring accuracy."/>
36 </section>
37 </inputs>
38 <outputs>
39 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} Comparison summary"/>
40 </outputs>
41 <tests>
42 <test><!-- relative abundance test -->
43 <param name="observed" value="observed_ra.biom" ftype="biom1"/>
44 <param name="expected" value="expected_ra.biom" ftype="biom1"/>
45 <output name="outfile" ftype="tabular">
46 <assert_contents>
47 <has_text_matching expression="file\tlabel\taccuracy"/>
48 <has_text text="sample1"/>
49 <has_text text="sample3"/>
50 <has_text text="sample2"/>
51 </assert_contents>
52 </output>
53 </test>
54 <test><!-- real counts test -->
55 <param name="observed" value="observed.biom" ftype="biom1"/>
56 <param name="expected" value="expected.biom" ftype="biom1"/>
57 <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>
58 <output name="outfile" ftype="tabular">
59 <assert_contents>
60 <has_text_matching expression="file\tlabel\taccuracy"/>
61 <has_text text="sample1"/>
62 <has_text text="sample3"/>
63 <has_text text="sample2"/>
64 </assert_contents>
65 </output>
66 </test>
67 <test><!-- all other switches test -->
68 <param name="observed" value="observed.biom" ftype="biom1"/>
69 <param name="expected" value="expected.biom" ftype="biom1"/>
70 <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>
71 <param name="compare_observations" value="--compare_observations"/>
72 <param name="normalize" value="--normalize"/>
73 <param name="limit_to_observed_observations" value="--limit_to_observed_observations"/>
74 <param name="shuffle_samples" value="--shuffle_samples"/>
75 <output name="outfile" ftype="tabular">
76 <assert_contents>
77 <has_text_matching expression="file\tlabel\taccuracy"/>
78 <has_text text="sample1"/>
79 <has_text text="sample3"/>
80 <has_text text="sample2"/>
81 </assert_contents>
82 </output>
83 </test>
84 </tests>
85 <help>
86 <![CDATA[
87 @PICRUST_OVERVIEW@
88
89 **Command Documentation**
90
91 Compare an observed table to an expected table using either relative abundance or real counts.
92
93 **Input files:**
94
95 **Observed table:** A table of observed relative abundances or real counts in .biom format.
96
97 **Expected table:** The expected table of relative abundances or real counts in .biom format.
98
99 **Output file:** Tab delimited file with various accuracy metrics.
100
101 **Optional Parameters:**
102
103 *compare observations*
104
105 Calculate accuracy values by comparing between observations (instead of between samples) [default: False]
106
107 *normalize*
108
109 Convert both expected and observed tables to relative abundances (instead of observations) [default: False]
110
111 *limit to expected observations*
112
113 Ignore observations that are not in the expected table[default: False]
114
115 *limit to observed observations*
116
117 Ignore observations that are not in the observed table[default: False]
118
119 *shuffle samples*
120
121 Shuffle samples ids randomly before measuring accuracy[default: False]
122
123 *not relative abundance scores*
124
125 Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN [default: False]
126
127 ]]>
128 </help>
129 <expand macro="citations"/>
130 </tool>