Mercurial > repos > iuc > mmuphin
changeset 1:23d58581f349 draft default tip
planemo upload for repository https://github.com/biobakery/MMUPHin commit 85ea7462e2b824c35b9d444f6dfced71e990a412
| author | iuc |
|---|---|
| date | Fri, 16 May 2025 12:56:52 +0000 |
| parents | 3938766e5135 |
| children | |
| files | macros.xml mmuphin.xml test-data/CRC_abd_corrected.tsv test-data/CRC_abd_corrected2.tsv test-data/CRC_abd_corrected3.tsv test-data/diagnostic.pdf test-data/diagnostic2.pdf test-data/diagnostic3.pdf |
| diffstat | 8 files changed, 14 insertions(+), 13 deletions(-) [+] |
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--- a/macros.xml Tue Feb 25 21:25:45 2025 +0000 +++ b/macros.xml Fri May 16 12:56:52 2025 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.16.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.2</token> <xml name="xrefs"> @@ -18,7 +18,7 @@ </xml> <xml name="citations"> <citations> - <citation type="doi"> 10.18129/B9.bioc.MMUPHin </citation> + <citation type="doi">10.18129/B9.bioc.MMUPHin</citation> </citations> </xml> </macros>
--- a/mmuphin.xml Tue Feb 25 21:25:45 2025 +0000 +++ b/mmuphin.xml Fri May 16 12:56:52 2025 +0000 @@ -65,7 +65,8 @@ # Save results into output files - write.table(result\$feature_abd_adj, file="$output", quote = FALSE, sep="\t") + write.table(result\$feature_abd_adj, file="$output", quote = FALSE, sep="\t", col.names=NA) + ]]></configfile> </configfiles> @@ -79,7 +80,7 @@ <param argument="pseudo_count" type="float" optional="true" label="Pseudo_count" help="Pseudo count to add feature_abd before the methods' log transformation. Default to the half of the minimal non-zero values in feature_abd" /> <param argument="conv" type="float" value="0.0001" min="0.000001" max="0.001" optional="true" label="Convergence threshold" help="Convergence threshold for the method's iterative algorithm for shrinking batch effect parameters."/> <param argument="maxit" type="float" optional="true" value="1000" label="Maximum number of iterations" help="Maximum number of iterations allowed for the method's iterative algorithm. Default to 1000"/> - <param argument="verbose" type="hidden" truevalue="verbose TRUE" falsevalue="verbose FALSE" checked="true" label="Print verbose information"/> + <param argument="verbose" type="hidden" value="False" label="Print verbose information"/> <param argument="diagnostic_plot" type="boolean" truevalue="diagnostic_plot TRUE" falsevalue="diagnostic_plot FALSE" checked="true" label="Generate diagnostic figure file"/> </section> </inputs> @@ -100,11 +101,11 @@ <param name="batch_input" value="29"/> <param name="covariates_input" value="4"/> <section name="additional_options"> - <param name="zero_inflation" value="TRUE"/> + <param name="zero_inflation" value="True"/> <param name="pseudo_count" value="3"/> <param name="conv" value="0.0001"/> <param name="maxit" value="1000"/> - <param name="diagnostic_plot" value="TRUE"/> + <param name="diagnostic_plot" value="True"/> </section> <output name="output" file="CRC_abd_corrected.tsv" ftype="tabular"/> <output name="diagnostic_plot_output" file="diagnostic.pdf" ftype="pdf"/> @@ -114,11 +115,11 @@ <param name="input_metadata" value="CRC_meta.tsv"/> <param name="batch_input" value="7"/> <section name="additional_options"> - <param name="zero_inflation" value="TRUE"/> + <param name="zero_inflation" value="True"/> <param name="pseudo_count" value="3"/> <param name="conv" value="0.0001"/> <param name="maxit" value="1000"/> - <param name="diagnostic_plot" value="TRUE"/> + <param name="diagnostic_plot" value="True"/> </section> <output name="output" file="CRC_abd_corrected2.tsv" ftype="tabular"/> <output name="diagnostic_plot_output" file="diagnostic2.pdf" ftype="pdf"/> @@ -129,11 +130,11 @@ <param name="batch_input" value="29"/> <param name="covariates_input" value="4,6"/> <section name="additional_options"> - <param name="zero_inflation" value="TRUE"/> + <param name="zero_inflation" value="True"/> <param name="pseudo_count" value="3"/> <param name="conv" value="0.0001"/> <param name="maxit" value="1000"/> - <param name="diagnostic_plot" value="TRUE"/> + <param name="diagnostic_plot" value="True"/> </section> <output name="output" file="CRC_abd_corrected3.tsv" ftype="tabular"/> <output name="diagnostic_plot_output" file="diagnostic3.pdf" ftype="pdf"/>
--- a/test-data/CRC_abd_corrected.tsv Tue Feb 25 21:25:45 2025 +0000 +++ b/test-data/CRC_abd_corrected.tsv Fri May 16 12:56:52 2025 +0000 @@ -1,4 +1,4 @@ -FengQ_2015.metaphlan_bugs_list.stool:SID31004 FengQ_2015.metaphlan_bugs_list.stool:SID31009 FengQ_2015.metaphlan_bugs_list.stool:SID31021 FengQ_2015.metaphlan_bugs_list.stool:SID31071 FengQ_2015.metaphlan_bugs_list.stool:SID31112 FengQ_2015.metaphlan_bugs_list.stool:SID31129 FengQ_2015.metaphlan_bugs_list.stool:SID31159 FengQ_2015.metaphlan_bugs_list.stool:SID31160 FengQ_2015.metaphlan_bugs_list.stool:SID31188 FengQ_2015.metaphlan_bugs_list.stool:SID31219 FengQ_2015.metaphlan_bugs_list.stool:SID31223 FengQ_2015.metaphlan_bugs_list.stool:SID31236 FengQ_2015.metaphlan_bugs_list.stool:SID31237 FengQ_2015.metaphlan_bugs_list.stool:SID31267 FengQ_2015.metaphlan_bugs_list.stool:SID31276 FengQ_2015.metaphlan_bugs_list.stool:SID31285 FengQ_2015.metaphlan_bugs_list.stool:SID31300 FengQ_2015.metaphlan_bugs_list.stool:SID31328 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--- a/test-data/CRC_abd_corrected2.tsv Tue Feb 25 21:25:45 2025 +0000 +++ b/test-data/CRC_abd_corrected2.tsv Fri May 16 12:56:52 2025 +0000 @@ -1,4 +1,4 @@ -FengQ_2015.metaphlan_bugs_list.stool:SID31004 FengQ_2015.metaphlan_bugs_list.stool:SID31009 FengQ_2015.metaphlan_bugs_list.stool:SID31021 FengQ_2015.metaphlan_bugs_list.stool:SID31071 FengQ_2015.metaphlan_bugs_list.stool:SID31112 FengQ_2015.metaphlan_bugs_list.stool:SID31129 FengQ_2015.metaphlan_bugs_list.stool:SID31159 FengQ_2015.metaphlan_bugs_list.stool:SID31160 FengQ_2015.metaphlan_bugs_list.stool:SID31188 FengQ_2015.metaphlan_bugs_list.stool:SID31219 FengQ_2015.metaphlan_bugs_list.stool:SID31223 FengQ_2015.metaphlan_bugs_list.stool:SID31236 FengQ_2015.metaphlan_bugs_list.stool:SID31237 FengQ_2015.metaphlan_bugs_list.stool:SID31267 FengQ_2015.metaphlan_bugs_list.stool:SID31276 FengQ_2015.metaphlan_bugs_list.stool:SID31285 FengQ_2015.metaphlan_bugs_list.stool:SID31300 FengQ_2015.metaphlan_bugs_list.stool:SID31328 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--- a/test-data/CRC_abd_corrected3.tsv Tue Feb 25 21:25:45 2025 +0000 +++ b/test-data/CRC_abd_corrected3.tsv Fri May 16 12:56:52 2025 +0000 @@ -1,4 +1,4 @@ -FengQ_2015.metaphlan_bugs_list.stool:SID31004 FengQ_2015.metaphlan_bugs_list.stool:SID31009 FengQ_2015.metaphlan_bugs_list.stool:SID31021 FengQ_2015.metaphlan_bugs_list.stool:SID31071 FengQ_2015.metaphlan_bugs_list.stool:SID31112 FengQ_2015.metaphlan_bugs_list.stool:SID31129 FengQ_2015.metaphlan_bugs_list.stool:SID31159 FengQ_2015.metaphlan_bugs_list.stool:SID31160 FengQ_2015.metaphlan_bugs_list.stool:SID31188 FengQ_2015.metaphlan_bugs_list.stool:SID31219 FengQ_2015.metaphlan_bugs_list.stool:SID31223 FengQ_2015.metaphlan_bugs_list.stool:SID31236 FengQ_2015.metaphlan_bugs_list.stool:SID31237 FengQ_2015.metaphlan_bugs_list.stool:SID31267 FengQ_2015.metaphlan_bugs_list.stool:SID31276 FengQ_2015.metaphlan_bugs_list.stool:SID31285 FengQ_2015.metaphlan_bugs_list.stool:SID31300 FengQ_2015.metaphlan_bugs_list.stool:SID31328 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