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changeset 0:bba4cafe21a8 draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compute_wilcoxon_test commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty
author bebatut
date Tue, 12 Apr 2016 02:56:51 -0400
parents
children ff9e8750bb26
files compute_wilcoxon_test.R compute_wilcoxon_test.xml test-data/input_file.txt test-data/output_file.txt tool_dependencies.xml
diffstat 5 files changed, 375 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_wilcoxon_test.R	Tue Apr 12 02:56:51 2016 -0400
@@ -0,0 +1,51 @@
+library('getopt')
+
+option_specification = matrix(c(
+  'input_file', 'a', 2, 'character',
+  'output_file', 'b', 2, 'character',
+  'column1_id', 'c', 2, 'integer',
+  'column2_id', 'd', 2, 'integer',
+  'alternative','e',2,'character',
+  'paired','f',2,'logical',
+  'exact','g',2,'logical',
+  'correct','h',2, 'logical',
+  'mu','i',2,'integer'
+), byrow=TRUE, ncol=4);
+
+options = getopt(option_specification);
+
+data = read.table(options$input_file, sep = '\t', h = T)
+
+column1_id = 1
+if(!is.null(options$column1_id)) column1_id = options$column1_id
+x = data[,column1_id]
+y = NULL
+if(!is.null(options$column2_id)) y = data[,options$column2_id]
+
+alternative = 'two.sided'
+if(!is.null(options$alternative)) alternative = options$alternative
+
+mu = 0
+if(!is.null(options$mu)) mu = options$mu
+
+paired = FALSE
+if(!is.null(options$paired)) paired = options$paired
+
+exact = NULL
+if(!is.null(options$exact)) exact = options$exact
+
+correct = TRUE
+if(!is.null(options$correct)) correct = options$correct
+
+test = wilcox.test(x = x, y = y, alternative = alternative, mu = mu, 
+    paired = paired, exact = exact, correct = correct)
+
+m = matrix(ncol = 2, nrow = 6)
+m[1,] = c('statistic',test$statistic)
+m[2,] = c('parameter',test$parameter)
+m[3,] = c('p.value',test$p.value)
+m[4,] = c('null.value',test$null.value)
+m[5,] = c('alternative',test$alternative)
+m[6,] = c('method',test$method)
+write.table(m, file = options$output_file, sep = "\t", quote = FALSE, 
+    row.names = FALSE, col.names = FALSE)
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_wilcoxon_test.xml	Tue Apr 12 02:56:51 2016 -0400
@@ -0,0 +1,90 @@
+<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">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>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_file.txt	Tue Apr 12 02:56:51 2016 -0400
@@ -0,0 +1,219 @@
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+METHANOGENESIS-PWY	0.0352711	0.00632509
+METHGLYUT-PWY	0.231264	0.0358341
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+METSYN-PWY	0.185879	0.0402475
+NAD-BIOSYNTHESIS-II	0.0539411	0.0498032
+NAGLIPASYN-PWY	0.0282235	0.00548584
+NONMEVIPP-PWY	0.0366808	0.00468516
+NONOXIPENT-PWY	0.333471	0.119833
+OANTIGEN-PWY	0.064821	0.0115185
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+P122-PWY	0.0986031	0.0184304
+P125-PWY	0.478315	0.170173
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+PANTOSYN-PWY	0.18209	0.0156617
+PENTOSE-P-PWY	0.205923	0.0327824
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+PPGPPMET-PWY	0.233335	0.12058
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+PWY-5913	0.0489618	0.0648256
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+PWY-6071	0.025905	0.00177062
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_file.txt	Tue Apr 12 02:56:51 2016 -0400
@@ -0,0 +1,6 @@
+statistic	22435
+parameter	parameter
+p.value	2.0527634209064e-29
+null.value	0
+alternative	two.sided
+method	Wilcoxon signed rank test with continuity correction
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Apr 12 02:56:51 2016 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.1">
+        <repository changeset_revision="9f31a291b305" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="getopt" version="1.20.0">
+        <repository changeset_revision="a0851e07e3ac" name="package_r_3_2_1_getopt_1_20_0" owner="bebatut" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>