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comparison mmuphin.xml @ 1:23d58581f349 draft default tip

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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
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0:3938766e5135 1:23d58581f349
63 control=controls 63 control=controls
64 ) 64 )
65 65
66 # Save results into output files 66 # Save results into output files
67 67
68 write.table(result\$feature_abd_adj, file="$output", quote = FALSE, sep="\t") 68 write.table(result\$feature_abd_adj, file="$output", quote = FALSE, sep="\t", col.names=NA)
69
69 ]]></configfile> 70 ]]></configfile>
70 </configfiles> 71 </configfiles>
71 72
72 <inputs> 73 <inputs>
73 <param name="input_data" type="data" format="tabular" label="Abundance (or features) file" help="TSV file where columns represent samples and rows include abundance values for features such as taxa, genes, or other biological entities across those samples."/> 74 <param name="input_data" type="data" format="tabular" label="Abundance (or features) file" help="TSV file where columns represent samples and rows include abundance values for features such as taxa, genes, or other biological entities across those samples."/>
77 <section name="additional_options" title="Additional Options" expanded="true"> 78 <section name="additional_options" title="Additional Options" expanded="true">
78 <param argument="zero_inflation" type="boolean" truevalue="zero_inflation TRUE" falsevalue="zero_inflation FALSE" checked="true" label="Run zero-inflated model"/> 79 <param argument="zero_inflation" type="boolean" truevalue="zero_inflation TRUE" falsevalue="zero_inflation FALSE" checked="true" label="Run zero-inflated model"/>
79 <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" /> 80 <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" />
80 <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."/> 81 <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."/>
81 <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"/> 82 <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"/>
82 <param argument="verbose" type="hidden" truevalue="verbose TRUE" falsevalue="verbose FALSE" checked="true" label="Print verbose information"/> 83 <param argument="verbose" type="hidden" value="False" label="Print verbose information"/>
83 <param argument="diagnostic_plot" type="boolean" truevalue="diagnostic_plot TRUE" falsevalue="diagnostic_plot FALSE" checked="true" label="Generate diagnostic figure file"/> 84 <param argument="diagnostic_plot" type="boolean" truevalue="diagnostic_plot TRUE" falsevalue="diagnostic_plot FALSE" checked="true" label="Generate diagnostic figure file"/>
84 </section> 85 </section>
85 </inputs> 86 </inputs>
86 87
87 <outputs> 88 <outputs>
98 <param name="input_data" value="CRC_abd.tsv"/> 99 <param name="input_data" value="CRC_abd.tsv"/>
99 <param name="input_metadata" value="CRC_meta.tsv"/> 100 <param name="input_metadata" value="CRC_meta.tsv"/>
100 <param name="batch_input" value="29"/> 101 <param name="batch_input" value="29"/>
101 <param name="covariates_input" value="4"/> 102 <param name="covariates_input" value="4"/>
102 <section name="additional_options"> 103 <section name="additional_options">
103 <param name="zero_inflation" value="TRUE"/> 104 <param name="zero_inflation" value="True"/>
104 <param name="pseudo_count" value="3"/> 105 <param name="pseudo_count" value="3"/>
105 <param name="conv" value="0.0001"/> 106 <param name="conv" value="0.0001"/>
106 <param name="maxit" value="1000"/> 107 <param name="maxit" value="1000"/>
107 <param name="diagnostic_plot" value="TRUE"/> 108 <param name="diagnostic_plot" value="True"/>
108 </section> 109 </section>
109 <output name="output" file="CRC_abd_corrected.tsv" ftype="tabular"/> 110 <output name="output" file="CRC_abd_corrected.tsv" ftype="tabular"/>
110 <output name="diagnostic_plot_output" file="diagnostic.pdf" ftype="pdf"/> 111 <output name="diagnostic_plot_output" file="diagnostic.pdf" ftype="pdf"/>
111 </test> 112 </test>
112 <test expect_num_outputs="2"> 113 <test expect_num_outputs="2">
113 <param name="input_data" value="CRC_abd.tsv"/> 114 <param name="input_data" value="CRC_abd.tsv"/>
114 <param name="input_metadata" value="CRC_meta.tsv"/> 115 <param name="input_metadata" value="CRC_meta.tsv"/>
115 <param name="batch_input" value="7"/> 116 <param name="batch_input" value="7"/>
116 <section name="additional_options"> 117 <section name="additional_options">
117 <param name="zero_inflation" value="TRUE"/> 118 <param name="zero_inflation" value="True"/>
118 <param name="pseudo_count" value="3"/> 119 <param name="pseudo_count" value="3"/>
119 <param name="conv" value="0.0001"/> 120 <param name="conv" value="0.0001"/>
120 <param name="maxit" value="1000"/> 121 <param name="maxit" value="1000"/>
121 <param name="diagnostic_plot" value="TRUE"/> 122 <param name="diagnostic_plot" value="True"/>
122 </section> 123 </section>
123 <output name="output" file="CRC_abd_corrected2.tsv" ftype="tabular"/> 124 <output name="output" file="CRC_abd_corrected2.tsv" ftype="tabular"/>
124 <output name="diagnostic_plot_output" file="diagnostic2.pdf" ftype="pdf"/> 125 <output name="diagnostic_plot_output" file="diagnostic2.pdf" ftype="pdf"/>
125 </test> 126 </test>
126 <test expect_num_outputs="2"> 127 <test expect_num_outputs="2">
127 <param name="input_data" value="CRC_abd.tsv"/> 128 <param name="input_data" value="CRC_abd.tsv"/>
128 <param name="input_metadata" value="CRC_meta.tsv"/> 129 <param name="input_metadata" value="CRC_meta.tsv"/>
129 <param name="batch_input" value="29"/> 130 <param name="batch_input" value="29"/>
130 <param name="covariates_input" value="4,6"/> 131 <param name="covariates_input" value="4,6"/>
131 <section name="additional_options"> 132 <section name="additional_options">
132 <param name="zero_inflation" value="TRUE"/> 133 <param name="zero_inflation" value="True"/>
133 <param name="pseudo_count" value="3"/> 134 <param name="pseudo_count" value="3"/>
134 <param name="conv" value="0.0001"/> 135 <param name="conv" value="0.0001"/>
135 <param name="maxit" value="1000"/> 136 <param name="maxit" value="1000"/>
136 <param name="diagnostic_plot" value="TRUE"/> 137 <param name="diagnostic_plot" value="True"/>
137 </section> 138 </section>
138 <output name="output" file="CRC_abd_corrected3.tsv" ftype="tabular"/> 139 <output name="output" file="CRC_abd_corrected3.tsv" ftype="tabular"/>
139 <output name="diagnostic_plot_output" file="diagnostic3.pdf" ftype="pdf"/> 140 <output name="diagnostic_plot_output" file="diagnostic3.pdf" ftype="pdf"/>
140 </test> 141 </test>
141 </tests> 142 </tests>