Mercurial > repos > erasmus-medical-center > voom_transform

diff voom_transform.xml @ 0:c6a3a93a237e draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/voom_transform commit e7e72828395347db6ba45ad6b927cd551b5e9327
author erasmus-medical-center
date Wed, 25 Jan 2017 10:13:10 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/voom_transform.xml	Wed Jan 25 10:13:10 2017 -0500
@@ -0,0 +1,75 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="voom_transform" name="Voom transform" version="3.29.0-0">
+    <description>transform count data to fit linear modelling</description>
+    <requirements>
+        <requirement type="package" version="3.29.0">bioconductor-limma</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+    </requirements>
+    
+    <version_command>echo $(R --version | grep -i version | head -n 1)", Limma: "$(R --vanilla --slave -e "library(limma) ; cat(sessionInfo()\$otherPkgs\$limma\$Version)")</version_command>
+    
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript
+            #if str($include_rdata) == 'true'
+                --save
+            #end if
+            '${__tool_directory__}/voom_transform.R'
+            -e '${input_select.expression_matrix}'
+            -t '${output_matrix}'
+        
+        #if str($include_rdata) == 'true'
+            && cp '.RData' '$output_rdata'
+        #end if
+    
+    ]]></command>
+    
+    <inputs>
+        <conditional name="input_select">
+            <param name="input_format" type="select" label="Output format">
+                <option value="1">Single expression matrix (header + multi column)</option>
+                <!-- <option value="2">Count files (no header + 1 sample per file)</option>-->
+            </param>
+            
+            <when value="1">
+                <param name="expression_matrix" type="data" format="txt,tabular" />
+            </when>
+            <!-- 
+            <when value="2">
+                repeat / input type = multiple
+            </when>
+             -->
+        </conditional>
+        
+        <param name="include_rdata" type="boolean" truevalue="true" falsevalue="" label="Save RData object" />
+        
+        <!-- normalization param
+        -->
+        
+    </inputs>
+    
+    <outputs>
+        <data name="output_matrix" format="tabular"
+              label="${tool.name} on $on_string" />
+
+        <data name="output_rdata" format="RData" label="${tool.name} on $on_string (RData)">
+            <filter>str(include_rdata) in ['true', true]</filter>
+        </data>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_format" value="1" />
+            <param name="expression_matrix" value="em.txt" />
+             
+            <output name="output_matrix" value="em_transformed.txt" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+        
+    ]]></help>
+    
+    <citations>
+        <citation type="doi">10.1093/nar/gkv007</citation>
+    </citations>
+</tool>