| Previous changeset 2:faacef62bb54 (2024-04-29) Next changeset 4:f4580402a2a2 (2024-09-10) |
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Commit message:
planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5 |
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modified:
maaslin2.xml macros.xml |
| b |
| diff -r faacef62bb54 -r 43ccbef89f1d maaslin2.xml --- a/maaslin2.xml Mon Apr 29 10:33:48 2024 +0000 +++ b/maaslin2.xml Wed Jun 26 09:40:13 2024 +0000 |
| [ |
| b'@@ -64,6 +64,10 @@\n #if $fixed_effects\n --fixed_effects \\$fixed_effects\n #end if\n+#if $reference\n+ --reference \'$reference\'\n+#end if\n+ \n #if $additional_options.correction\n --correction \'$additional_options.correction\'\n #end if\n@@ -73,23 +77,24 @@\n --heatmap_first_n \'$output.heatmap_first_n\'\n #end if\n $output.plot_scatter\n- --cores \\${GALAXY_SLOTS:-4}\n+ --cores 1\n \'input_data.tsv\'\n \'input_metadata.tsv\'\n \'outputFolder\'\n &&\n-cd outputFolder && mkdir -p figures/ && cp *.pdf figures\n+zip -r out.zip outputFolder &&\n+cd outputFolder && \n+mkdir -p figures/ && \n+cp *.pdf figures\n+\n \n ]]></command>\n <inputs>\n <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>\n <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>\n <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " />\n- \t\t\n <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects, Default: None" />\n- \t\n- \n- \t\n+ <param argument="--reference" type="text" label="Reference" help="Reference for a variable with more than two levels provided as a string of \'variable,reference\' comma delimited for multiple variables. " />\n <section name="additional_options" title="Additional Options" expanded="true">\n <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>\n <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/>\n@@ -114,10 +119,13 @@\n <option value="ZINB">ZINB</option>\n </param>\n <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value, Default: BH ">\n- \n <option value="BH">Benjamini-Hochberg(BH)</option>\n <option value="BY">Benjamini-Yekutieli(BY)</option>\n- </param>\n+ <option value="Bonferroni">Bonferroni</option>\n+ <option value="Holm">Holm</option>\n+ <option value="Hochberg">Hochberg</option>\n+ <option value="Hommel">Hommel</option>\n+\t </param>\n <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on the same scale"/>\n </section> \n <section name="output" title="Set Plotting Output" expanded="true">\n@@ -127,10 +135,11 @@\n <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/> \n </section> \n </inputs>\n- <outputs> \n+ <outputs>\n+ <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" />\n <data name="all_results" format="tabular" from_work_dir="outputFolder/all_results.tsv" label="All results ordered by increasing q-value"/>\n <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/>\n- <data name="residuals" format="rdata" from_work_dir="outputFolder/residuals.rds" label="Data frame with residuals for each feature"> \n+ '..b' \n <section name="additional_options">\n <param name="min_abundance" value="0.0"/>\n <param name="min_prevalence" value="0.1"/>\n@@ -354,23 +379,28 @@\n <param name="plot_scatter" value="true"/>\n <param name="residuals_output" value="true"/>\n </section>\n+ <output name="archive_output">\n+ <assert_contents>\n+ <has_size value="8567935" delta="1000000" />\n+ </assert_contents>\n+ </output>\n <output name="all_results">\n <assert_contents>\n <has_text text="feature"/>\n- <has_n_lines n="8092"/>\n+ <has_n_lines n="175" delta="10"/>\n <has_n_columns n="9"/>\n </assert_contents>\n </output>\n <output name="significant_results">\n <assert_contents>\n- <has_text text="subject"/>\n- <has_n_lines n="216" delta="5"/>\n+ <has_text text="dysbiosisnonIBD"/>\n+ <has_n_lines n="95" delta="5"/>\n <has_n_columns n="9"/>\n </assert_contents>\n </output>\n <output name="residuals">\n <assert_contents>\n- <has_size value="671142" delta="1000"/>\n+ <has_size value="434087"/>\n </assert_contents>\n </output>\n <output_collection name="figures_pdfs" type="list">\n@@ -381,53 +411,8 @@\n </element> \n </output_collection>\n </test> \n- <test expect_num_outputs="5">\n- <param name="input_data" value="HMP2_taxonomy.tsv"/>\n- <param name="input_metadata" value="HMP2_metadata.tsv"/>\n- \n- <section name="additional_options">\n- <param name="min_abundance" value="0.0"/>\n- <param name="min_prevalence" value="0.1"/>\n- <param name="max_significance" value="0.25"/>\n- <param name="normalization" value="TSS"/>\n- <param name="transform" value="LOG"/>\n- <param name="analysis_method" value="LM"/>\n- <param name="correction" value="BH"/>\n- <param name="standardize" value="True"/>\n- </section>\n- <section name="output">\n- <param name="plot_heatmap" value="true"/>\n- <param name="heatmap_first_n" value="50"/>\n- <param name="plot_scatter" value="true"/>\n- <param name="residuals_output" value="true"/>\n- </section>\n- <output name="all_results">\n- <assert_contents>\n- <has_text text="feature"/>\n- <has_n_lines n="8092"/>\n- <has_n_columns n="9"/>\n- </assert_contents>\n- </output>\n- <output name="significant_results">\n- <assert_contents>\n- <has_text text="subject"/>\n- <has_n_lines n="880"/>\n- <has_n_columns n="9"/>\n- </assert_contents>\n- </output>\n- <output name="residuals">\n- <assert_contents>\n- <has_size value="670759" delta="1000"/>\n- </assert_contents>\n- </output>\n- <output_collection name="figures_pdfs" type="list">\n- <element name="heatmap.pdf" ftype="pdf">\n- <assert_contents>\n- <has_size value="7900" delta="1000" />\n- </assert_contents>\n- </element> \n- </output_collection>\n- </test> \n+ \n+ \n </tests>\n <help><![CDATA[\n @HELP_HEADER@\n' |
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| diff -r faacef62bb54 -r 43ccbef89f1d macros.xml --- a/macros.xml Mon Apr 29 10:33:48 2024 +0000 +++ b/macros.xml Wed Jun 26 09:40:13 2024 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">0.99.12</token> + <token name="@TOOL_VERSION@">1.16.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.01</token> <xml name="edam_ontology"> @@ -17,7 +17,8 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="@TOOL_VERSION@">maaslin2</requirement> + <requirement type="package" version="@TOOL_VERSION@">bioconductor-maaslin2</requirement> + <requirement type="package" version="3.0">zip</requirement> <yield/> </requirements> </xml> |