Mercurial > repos > bebatut > compute_wilcoxon_test
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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 3395621548e21ec7eb27207827ccdf6726132d26-dirty
author | bebatut |
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date | Thu, 14 Apr 2016 10:37:32 -0400 |
parents | bba4cafe21a8 |
children | 309fac5c91d8 |
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<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 --output_file $output_file --column1_id $column1_id #if $add_data.test == 'true': --column2_id $add_data.column2_id --paired $add_data.paired #end if --alternative "$alternative" --mu $mu --exact $exact --correct $correct ]]></command> <inputs> <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/> <param name="column1_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column1_id)"/> <conditional name="add_data"> <param name="test" label="Add a new column?" type="select" help="(--alternative)"> <option value="true" selected="True">Yes</option> <option value="false">No</option> </param> <when value="true"> <param name="column2_id" type="data_column" data_ref="input_file" label="Column containing data" multiple="false" numerical="true" help="(--column2_id)"/> <param name="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Paired datasets?" checked="false" help="(--paired)"/> </when> <when value="false" /> </conditional> <param name="alternative" label="Alternative hypothesis" type="select" help="(--alternative)"> <option value="two.sided" selected="True">Two sided</option> <option value="greater">Greater</option> <option value="less">Less</option> </param> <param name="mu" type="integer" value="0" label="Optional parameter used to form the null hypothesis" help="(--mu)"/> <param name="exact" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Compute an exact p-value?" checked="false" help="(--exact)"/> <param name="correct" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Apply a continuity correction in the normal approximation for the p-value?" checked="true" help="(--correct)"/> </inputs> <outputs> <data name="output_file" format="text" label="${tool.name} on ${on_string}: Wilcox test result" /> </outputs> <tests> <param name="input_file" value="input_file.txt" /> <param name="column1_id" value="2" /> <param name="test" value="true" /> <param name="column2_id" value="3" /> <param name="paired" value="TRUE" /> <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" value="output_file.txt" /> </tests> <help><![CDATA[ **What it does** This tool compute a Wilcoxon test with R's wilcox.test function. ]]></help> <citations> </citations> </tool>