| Previous changeset 1:ef2cace85809 (2024-03-13) Next changeset 3:43ccbef89f1d (2024-06-26) |
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Commit message:
planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3 |
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modified:
maaslin2.xml macros.xml |
| b |
| diff -r ef2cace85809 -r faacef62bb54 maaslin2.xml --- a/maaslin2.xml Wed Mar 13 10:32:52 2024 +0000 +++ b/maaslin2.xml Mon Apr 29 10:33:48 2024 +0000 |
| [ |
| b'@@ -7,6 +7,34 @@\n <expand macro="xrefs"/>\n <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n+ \n+## get column names of fixed and random effect from the input file, since galaxy \n+## can only return indices with type="data_column" \n+## using awk so that the file is only parsed on command line execution\n+\n+#if $fixed_effects\n+#set idx = []\n+#for $i in $fixed_effects:\n+ #silent idx.append(f\'${i}\')\n+#end for\n+#set idx_for_awk = \',\'.join(idx)\n+\n+fixed_effects=`awk -v OFS=\',\' -F"\\t" \'NR == 1 { print $idx_for_awk}\' \'$input_metadata\'` &&\n+echo \'Assigned fixed effects as:\' \\$fixed_effects &&\n+#end if\n+\n+\n+#if $random_effects\n+#set idx = []\n+#for $i in $random_effects:\n+ #silent idx.append(f\'${i}\')\n+#end for\n+#set idx_for_awk = \',\'.join(idx)\n+\n+random_effects=`awk -v OFS=\',\' -F"\\t" \'NR == 1 { print $idx_for_awk}\' \'$input_metadata\'` &&\n+echo \'Assigned random effects as:\' \\$random_effects &&\n+#end if\n+\n ln -s \'$input_data\' \'input_data.tsv\'\n &&\n ln -s \'$input_metadata\' \'input_metadata.tsv\'\n@@ -31,10 +59,10 @@\n --analysis_method \'$additional_options.analysis_method\'\n #end if\n #if $random_effects\n- --random_effects \'$random_effects\'\n+ --random_effects \\$random_effects\n #end if\n #if $fixed_effects\n- --fixed_effects \'$fixed_effects\'\n+ --fixed_effects \\$fixed_effects\n #end if\n #if $additional_options.correction\n --correction \'$additional_options.correction\'\n@@ -51,19 +79,17 @@\n \'outputFolder\'\n &&\n cd outputFolder && mkdir -p figures/ && cp *.pdf figures\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="select" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects">\n- <option value="diagnosis" selected="true">diagnosis</option>\n- <option value="dysbiosisnonIBD" selected="true">dysbiosisnonIBD</option>\n- <option value="dysbiosisUC" selected="true">dysbiosisUC</option>\n- <option value="dysbiosisCD" selected="true">dysbiosisCD</option>\n- <option value="antibiotics" selected="true">antibiotics</option>\n- <option value="age" selected="true">age</option>\n- </param> \n- <param argument="--random_effects" type="text" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects"/> \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 <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@@ -87,7 +113,11 @@\n <option value="NEGBIN">NEGBIN</option>\n <option value="ZINB">ZINB</option>\n </param>\n- <param argument="--correction" type="text" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value"/>'..b'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="216" 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+ </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="7000" delta="1000" />\n+ </assert_contents>\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 </tests>\n <help><![CDATA[\n @HELP_HEADER@\n@@ -347,6 +471,9 @@\n - It only includes associations with q-values <= to the threshold.\n - Data frame with residuals for each feature (R data file)\n - This file contains a data frame with residuals for each feature.\n+ \n+Correction methods to compute the q-value : https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust\n+\n 2- Visualization output files\n - Heatmap of the significant associations (PDF file)\n - This file contains a heatmap of the significant associations.\n' |
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| diff -r ef2cace85809 -r faacef62bb54 macros.xml --- a/macros.xml Wed Mar 13 10:32:52 2024 +0000 +++ b/macros.xml Mon Apr 29 10:33:48 2024 +0000 |
| b |
| @@ -21,4 +21,4 @@ <yield/> </requirements> </xml> - </macros> \ No newline at end of file + </macros> |