Mercurial > repos > bebatut > compute_wilcoxon_test
diff compute_wilcoxon_test.xml @ 0:2a8acb4c0afc draft default tip
planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 450b58f2de19b05cd05c27ae77376fb1b71f5646
| author | bebatut |
|---|---|
| date | Thu, 21 Apr 2016 04:21:13 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compute_wilcoxon_test.xml Thu Apr 21 04:21:13 2016 -0400 @@ -0,0 +1,94 @@ +<tool id="compute_wilcoxon_test" name="Compute Wilcoxon test" version="0.1.0"> + <description>with R</description> + + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + </requirements> + + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + + <version_command></version_command> + + <command><![CDATA[ + Rscript $__tool_directory__/compute_wilcoxon_test.R + --input_file $input_file + --header $header + --output_file $output_file + --column1_id $column1_id + + #if $add_column.add_column_test == "true": + --column2_id $add_column.column2_id + --paired $add_column.paired + #end if + + --alternative "$alternative" + --mu $mu + + --exact $exact + --correct $correct + + ]]></command> + + <inputs> + <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/> + + <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/> + + <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/> + + <conditional name="add_column"> + <param name="add_column_test" label="Add a new column?" type="select" help="(--alternative)"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/> + <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/> + </when> + <when value="false" /> + </conditional> + + <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)"> + <option value="two.sided" selected="true">Two sided</option> + <option value="greater">Greater</option> + <option value="less">Less</option> + </param> + <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/> + + <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/> + <param name="correct" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Apply a continuity correction in the normal approximation for the p-value?" checked="true" help="(--correct)"/> + </inputs> + + <outputs> + <data name="output_file" format="txt" label="${tool.name} on ${on_string}: Wilcox test result" /> + </outputs> + + <tests> + <test> + <param name="input_file" ftype="tabular" value="input_file.txt"/> + <param name="header" value="TRUE"/> + <param name="column1_id" value="3"/> + <param name="add_column_test" value="true"/> + <param name="column2_id" value="5"/> + <param name="paired" value="FALSE"/> + <param name="alternative" value="two.sided"/> + <param name="mu" value="0"/> + <param name="exact" value="FALSE"/> + <param name="correct" value="TRUE"/> + <output name="output_file" file="two_sided_two_columns_test_output.txt"/> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +This tool compute a Wilcoxon test with R's wilcox.test function. + ]]></help> + + <citations> + </citations> +</tool>