Mercurial > repos > iuc > picrust_compare_biom
comparison compare_biom.xml @ 3:9168545e09df draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
author | iuc |
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date | Sat, 18 Dec 2021 16:08:32 +0000 |
parents | 43244ad9e7ef |
children | 8e2ac1b8f70a |
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2:0ba7dfaa941d | 3:9168545e09df |
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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@ |