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comparison compare_biom.xml @ 3:9168545e09df draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
author iuc
date Sat, 18 Dec 2021 16:08:32 +0000
parents 43244ad9e7ef
children 8e2ac1b8f70a
comparison
equal deleted inserted replaced
2:0ba7dfaa941d 3:9168545e09df
1 <tool id="picrust_compare_biom" name="Compare BIOM tables" version="@WRAPPER_VERSION@.0"> 1 <tool id="picrust_compare_biom" name="Compare BIOM tables" version="@TOOL_VERSION@.1">
2 <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description> 2 <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 compare_biom.py 9 compare_biom.py
10 -e '$expected' 10 -e '$expected'
11 -o '$outfile' 11 -o '$outfile'
12 $not_relative_abundance_scores 12 $not_relative_abundance_scores
13 $advanced.compare_observations
13 $advanced.normalize 14 $advanced.normalize
14 $advanced.limit_to_observed_observations 15 $advanced.limit_to_observed_observations
15 $advanced.limit_to_expected_observations 16 $advanced.limit_to_expected_observations
16 $advanced.shuffle_samples 17 $advanced.shuffle_samples
17
18 '$observed' 18 '$observed'
19 ]]></command> 19 ]]></command>
20 <inputs> 20 <inputs>
21 <param name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/> 21 <param argument="-o" 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"/> 22 <param argument="-e" 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?" 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"/> 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"> 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" 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)."/> 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?" 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)."/> 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?" 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."/> 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?" 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."/> 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?" 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."/> 35 help="Shuffle samples ids randomly before measuring accuracy."/>
36 </section> 36 </section>
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} Comparison summary"/> 39 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/>
40 </outputs> 40 </outputs>
41 <tests> 41 <tests>
42 <test><!-- relative abundance test --> 42 <test><!-- relative abundance test -->
43 <param name="observed" value="observed_ra.biom" ftype="biom1"/> 43 <param name="observed" value="observed_ra.biom" ftype="biom1"/>
44 <param name="expected" value="expected_ra.biom" ftype="biom1"/> 44 <param name="expected" value="expected_ra.biom" ftype="biom1"/>
46 <assert_contents> 46 <assert_contents>
47 <has_text_matching expression="file\tlabel\taccuracy"/> 47 <has_text_matching expression="file\tlabel\taccuracy"/>
48 <has_text text="sample1"/> 48 <has_text text="sample1"/>
49 <has_text text="sample3"/> 49 <has_text text="sample3"/>
50 <has_text text="sample2"/> 50 <has_text text="sample2"/>
51 <has_n_lines n="4"/>
52 <has_n_columns n="16"/>
51 </assert_contents> 53 </assert_contents>
52 </output> 54 </output>
55 <assert_command>
56 <not_has_text text="--not_relative_abundance_scores"/>
57 <not_has_text text="--compare_observations"/>
58 <not_has_text text="--normalize"/>
59 <not_has_text text="--limit_to_observed_observations"/>
60 <not_has_text text="--limit_to_expected_observations"/>
61 <not_has_text text="--shuffle_samples"/>
62 </assert_command>
53 </test> 63 </test>
54 <test><!-- real counts test --> 64 <test><!-- real counts test -->
55 <param name="observed" value="observed.biom" ftype="biom1"/> 65 <param name="observed" value="observed.biom" ftype="biom1"/>
56 <param name="expected" value="expected.biom" ftype="biom1"/> 66 <param name="expected" value="expected.biom" ftype="biom1"/>
57 <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/> 67 <param name="not_relative_abundance_scores" value="true"/>
58 <output name="outfile" ftype="tabular"> 68 <output name="outfile" ftype="tabular">
59 <assert_contents> 69 <assert_contents>
60 <has_text_matching expression="file\tlabel\taccuracy"/> 70 <has_text_matching expression="file\tlabel\taccuracy"/>
61 <has_text text="sample1"/> 71 <has_text text="sample1"/>
62 <has_text text="sample3"/> 72 <has_text text="sample3"/>
63 <has_text text="sample2"/> 73 <has_text text="sample2"/>
74 <has_n_lines n="4"/>
75 <has_n_columns n="16"/>
64 </assert_contents> 76 </assert_contents>
65 </output> 77 </output>
78 <assert_command>
79 <has_text text="--not_relative_abundance_scores"/>
80 <not_has_text text="--compare_observations"/>
81 <not_has_text text="--normalize"/>
82 <not_has_text text="--limit_to_observed_observations"/>
83 <not_has_text text="--limit_to_expected_observations"/>
84 <not_has_text text="--shuffle_samples"/>
85 </assert_command>
66 </test> 86 </test>
67 <test><!-- all other switches test --> 87 <test><!-- all other switches test -->
68 <param name="observed" value="observed.biom" ftype="biom1"/> 88 <param name="observed" value="observed.biom" ftype="biom1"/>
69 <param name="expected" value="expected.biom" ftype="biom1"/> 89 <param name="expected" value="expected.biom" ftype="biom1"/>
70 <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/> 90 <param name="not_relative_abundance_scores" value="true"/>
71 <param name="compare_observations" value="--compare_observations"/> 91 <section name="advanced">
72 <param name="normalize" value="--normalize"/> 92 <param name="compare_observations" value="true"/>
73 <param name="limit_to_observed_observations" value="--limit_to_observed_observations"/> 93 <param name="normalize" value="true"/>
74 <param name="shuffle_samples" value="--shuffle_samples"/> 94 <param name="limit_to_observed_observations" value="true"/>
95 <param name="limit_to_expected_observations" value="true"/>
96 <param name="shuffle_samples" value="true"/>
97 </section>
75 <output name="outfile" ftype="tabular"> 98 <output name="outfile" ftype="tabular">
76 <assert_contents> 99 <assert_contents>
77 <has_text_matching expression="file\tlabel\taccuracy"/> 100 <has_text_matching expression="file\tlabel\taccuracy"/>
78 <has_text text="sample1"/> 101 <has_text text="K00005"/>
79 <has_text text="sample3"/> 102 <has_text text="K00004"/>
80 <has_text text="sample2"/> 103 <has_text text="K00003"/>
104 <has_n_lines n="6"/>
105 <has_n_columns n="16"/>
81 </assert_contents> 106 </assert_contents>
82 </output> 107 </output>
108 <assert_command>
109 <has_text text="--not_relative_abundance_scores"/>
110 <has_text text="--compare_observations"/>
111 <has_text text="--normalize"/>
112 <has_text text="--limit_to_observed_observations"/>
113 <has_text text="--limit_to_expected_observations"/>
114 <has_text text="--shuffle_samples"/>
115 </assert_command>
83 </test> 116 </test>
84 </tests> 117 </tests>
85 <help> 118 <help>
86 <![CDATA[ 119 <![CDATA[
87 @PICRUST_OVERVIEW@ 120 @PICRUST_OVERVIEW@