Mercurial > repos > iuc > picrust_compare_biom
changeset 3:9168545e09df draft
"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 | 0ba7dfaa941d |
| children | 8e2ac1b8f70a |
| files | compare_biom.xml macros.xml |
| diffstat | 2 files changed, 55 insertions(+), 22 deletions(-) [+] |
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--- a/compare_biom.xml Thu Nov 28 15:54:42 2019 -0500 +++ b/compare_biom.xml Sat Dec 18 16:08:32 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@WRAPPER_VERSION@.0"> +<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@TOOL_VERSION@.1"> <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description> <macros> <import>macros.xml</import> @@ -10,33 +10,33 @@ -e '$expected' -o '$outfile' $not_relative_abundance_scores + $advanced.compare_observations $advanced.normalize $advanced.limit_to_observed_observations $advanced.limit_to_expected_observations $advanced.shuffle_samples - '$observed' ]]></command> <inputs> - <param name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/> - <param name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/> - <param argument="not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?" + <param argument="-o" name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/> + <param argument="-e" name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/> + <param argument="--not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?" help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/> <section name="advanced" title="Advanced parameters" expanded="false"> - <param argument="compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations" + <param argument="--compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations" help="Calculate accuracy values by comparing between observations (instead of between samples)."/> - <param argument="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?" + <param argument="--normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?" help="Convert both expected and observed tables to relative abundances (instead of observations)."/> - <param argument="limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?" + <param argument="--limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?" help="Ignore observations that are not in the observed table."/> - <param argument="limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?" + <param argument="--limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?" help="Ignore observations that are not in the expected table."/> - <param argument="shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?" + <param argument="--shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?" help="Shuffle samples ids randomly before measuring accuracy."/> </section> </inputs> <outputs> - <data format="tabular" name="outfile" label="${tool.name} on ${on_string} Comparison summary"/> + <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test><!-- relative abundance test --> @@ -48,38 +48,71 @@ <has_text text="sample1"/> <has_text text="sample3"/> <has_text text="sample2"/> + <has_n_lines n="4"/> + <has_n_columns n="16"/> </assert_contents> </output> + <assert_command> + <not_has_text text="--not_relative_abundance_scores"/> + <not_has_text text="--compare_observations"/> + <not_has_text text="--normalize"/> + <not_has_text text="--limit_to_observed_observations"/> + <not_has_text text="--limit_to_expected_observations"/> + <not_has_text text="--shuffle_samples"/> + </assert_command> </test> <test><!-- real counts test --> <param name="observed" value="observed.biom" ftype="biom1"/> <param name="expected" value="expected.biom" ftype="biom1"/> - <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/> + <param name="not_relative_abundance_scores" value="true"/> <output name="outfile" ftype="tabular"> <assert_contents> <has_text_matching expression="file\tlabel\taccuracy"/> <has_text text="sample1"/> <has_text text="sample3"/> <has_text text="sample2"/> + <has_n_lines n="4"/> + <has_n_columns n="16"/> </assert_contents> </output> + <assert_command> + <has_text text="--not_relative_abundance_scores"/> + <not_has_text text="--compare_observations"/> + <not_has_text text="--normalize"/> + <not_has_text text="--limit_to_observed_observations"/> + <not_has_text text="--limit_to_expected_observations"/> + <not_has_text text="--shuffle_samples"/> + </assert_command> </test> <test><!-- all other switches test --> <param name="observed" value="observed.biom" ftype="biom1"/> <param name="expected" value="expected.biom" ftype="biom1"/> - <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/> - <param name="compare_observations" value="--compare_observations"/> - <param name="normalize" value="--normalize"/> - <param name="limit_to_observed_observations" value="--limit_to_observed_observations"/> - <param name="shuffle_samples" value="--shuffle_samples"/> + <param name="not_relative_abundance_scores" value="true"/> + <section name="advanced"> + <param name="compare_observations" value="true"/> + <param name="normalize" value="true"/> + <param name="limit_to_observed_observations" value="true"/> + <param name="limit_to_expected_observations" value="true"/> + <param name="shuffle_samples" value="true"/> + </section> <output name="outfile" ftype="tabular"> <assert_contents> <has_text_matching expression="file\tlabel\taccuracy"/> - <has_text text="sample1"/> - <has_text text="sample3"/> - <has_text text="sample2"/> + <has_text text="K00005"/> + <has_text text="K00004"/> + <has_text text="K00003"/> + <has_n_lines n="6"/> + <has_n_columns n="16"/> </assert_contents> </output> + <assert_command> + <has_text text="--not_relative_abundance_scores"/> + <has_text text="--compare_observations"/> + <has_text text="--normalize"/> + <has_text text="--limit_to_observed_observations"/> + <has_text text="--limit_to_expected_observations"/> + <has_text text="--shuffle_samples"/> + </assert_command> </test> </tests> <help>
--- a/macros.xml Thu Nov 28 15:54:42 2019 -0500 +++ b/macros.xml Sat Dec 18 16:08:32 2021 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">1.1.1</token> + <token name="@TOOL_VERSION@">1.1.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="1.1.1">picrust</requirement> @@ -77,7 +77,7 @@ For more information please visit: - PICRUSt Documentation: https://picrust.github.io/picrust/ -- PICRUSt GitHub: http://picrust.github.com/ +- PICRUSt GitHub: https://github.com/picrust/picrust/ - PICRUSt Support: https://groups.google.com/d/forum/picrust-users **Reference Data**