| Previous changeset 2:0ba7dfaa941d (2019-11-28) Next changeset 4:8e2ac1b8f70a (2024-02-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f" |
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modified:
compare_biom.xml macros.xml |
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| diff -r 0ba7dfaa941d -r 9168545e09df compare_biom.xml --- a/compare_biom.xml Thu Nov 28 15:54:42 2019 -0500 +++ b/compare_biom.xml Sat Dec 18 16:08:32 2021 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@WRAPPER_VERSION@.0">\n+<tool id="picrust_compare_biom" name="Compare BIOM tables" version="@TOOL_VERSION@.1">\n <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description>\n <macros>\n <import>macros.xml</import>\n@@ -10,33 +10,33 @@\n -e \'$expected\'\n -o \'$outfile\'\n $not_relative_abundance_scores\n+ $advanced.compare_observations\n $advanced.normalize\n $advanced.limit_to_observed_observations\n $advanced.limit_to_expected_observations\n $advanced.shuffle_samples\n-\n \'$observed\'\n ]]></command>\n <inputs>\n- <param name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/>\n- <param name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/>\n- <param argument="not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?"\n+ <param argument="-o" name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/>\n+ <param argument="-e" name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/>\n+ <param argument="--not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?"\n help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/>\n <section name="advanced" title="Advanced parameters" expanded="false">\n- <param argument="compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations"\n+ <param argument="--compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations"\n help="Calculate accuracy values by comparing between observations (instead of between samples)."/>\n- <param argument="normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?"\n+ <param argument="--normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?"\n help="Convert both expected and observed tables to relative abundances (instead of observations)."/>\n- <param argument="limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?"\n+ <param argument="--limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?"\n help="Ignore observations that are not in the observed table."/>\n- <param argument="limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?"\n+ <param argument="--limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?"\n help="Ignore observations that are not in the expected table."/>\n- <param argument="shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?"\n+ <param argument="--shuffle_samples" type="boolean" trueva'..b' <has_n_columns n="16"/>\n </assert_contents>\n </output>\n+ <assert_command>\n+ <not_has_text text="--not_relative_abundance_scores"/>\n+ <not_has_text text="--compare_observations"/>\n+ <not_has_text text="--normalize"/>\n+ <not_has_text text="--limit_to_observed_observations"/>\n+ <not_has_text text="--limit_to_expected_observations"/>\n+ <not_has_text text="--shuffle_samples"/>\n+ </assert_command>\n </test>\n <test><!-- real counts test -->\n <param name="observed" value="observed.biom" ftype="biom1"/>\n <param name="expected" value="expected.biom" ftype="biom1"/>\n- <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>\n+ <param name="not_relative_abundance_scores" value="true"/>\n <output name="outfile" ftype="tabular">\n <assert_contents>\n <has_text_matching expression="file\\tlabel\\taccuracy"/>\n <has_text text="sample1"/>\n <has_text text="sample3"/>\n <has_text text="sample2"/>\n+ <has_n_lines n="4"/>\n+ <has_n_columns n="16"/>\n </assert_contents>\n </output>\n+ <assert_command>\n+ <has_text text="--not_relative_abundance_scores"/>\n+ <not_has_text text="--compare_observations"/>\n+ <not_has_text text="--normalize"/>\n+ <not_has_text text="--limit_to_observed_observations"/>\n+ <not_has_text text="--limit_to_expected_observations"/>\n+ <not_has_text text="--shuffle_samples"/>\n+ </assert_command>\n </test>\n <test><!-- all other switches test -->\n <param name="observed" value="observed.biom" ftype="biom1"/>\n <param name="expected" value="expected.biom" ftype="biom1"/>\n- <param name="not_relative_abundance_scores" value="--not_relative_abundance_scores"/>\n- <param name="compare_observations" value="--compare_observations"/>\n- <param name="normalize" value="--normalize"/>\n- <param name="limit_to_observed_observations" value="--limit_to_observed_observations"/>\n- <param name="shuffle_samples" value="--shuffle_samples"/>\n+ <param name="not_relative_abundance_scores" value="true"/>\n+ <section name="advanced">\n+ <param name="compare_observations" value="true"/>\n+ <param name="normalize" value="true"/>\n+ <param name="limit_to_observed_observations" value="true"/>\n+ <param name="limit_to_expected_observations" value="true"/>\n+ <param name="shuffle_samples" value="true"/>\n+ </section>\n <output name="outfile" ftype="tabular">\n <assert_contents>\n <has_text_matching expression="file\\tlabel\\taccuracy"/>\n- <has_text text="sample1"/>\n- <has_text text="sample3"/>\n- <has_text text="sample2"/>\n+ <has_text text="K00005"/>\n+ <has_text text="K00004"/>\n+ <has_text text="K00003"/>\n+ <has_n_lines n="6"/>\n+ <has_n_columns n="16"/>\n </assert_contents>\n </output>\n+ <assert_command>\n+ <has_text text="--not_relative_abundance_scores"/>\n+ <has_text text="--compare_observations"/>\n+ <has_text text="--normalize"/>\n+ <has_text text="--limit_to_observed_observations"/>\n+ <has_text text="--limit_to_expected_observations"/>\n+ <has_text text="--shuffle_samples"/>\n+ </assert_command>\n </test>\n </tests>\n <help>\n' |
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| diff -r 0ba7dfaa941d -r 9168545e09df macros.xml --- a/macros.xml Thu Nov 28 15:54:42 2019 -0500 +++ b/macros.xml Sat Dec 18 16:08:32 2021 +0000 |
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| @@ -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** |