diff dexseq.xml @ 22:71cb8c5ae8bd draft

Uploaded

--- a/dexseq.xml	Thu Sep 03 11:26:08 2015 -0400
+++ b/dexseq.xml	Tue Sep 22 11:24:46 2015 -0400
@@ -11,7 +11,7 @@
         #import json
         Rscript $__tool_directory__/dexseq.R
             -o "$dexseq_out"
-            -p 12
+            -p 6
             #set $temp_factor_names = list()
             #for $factor in $rep_factorName:
                 #set $temp_factor = list()
@@ -49,7 +49,7 @@
            description="An undefined error occured, please check your intput carefully and contact your administrator." />
     </stdio>
     <inputs>
-        <param name="gtf" type="data" label="GTF file created from dexseq_count tool"/>
+        <param name="gtf" type="data" label="GTF file created from DEXSeq-Count tool"/>
         <repeat name="rep_factorName" title="Factor" min="1">
             <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
                 help="Only letters, numbers and underscores will be retained in this field">
@@ -79,7 +79,78 @@
             <filter>report == True</filter>
         </data>
     </outputs>
+    
     <code file="dexseq_helper.py" />
+    <tests>
+        <test>
+            <param name="gtf" value="flattened.filtered.gtf" ftype="bed"/>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="condition" ftype="bed"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="knockdown"/>
+                    <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="knockdown"/>
+                    <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="knockdown"/>
+                    <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
+                </repeat>
+            </repeat>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="libtype" ftype="bed"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="singleend"/>
+                    <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="singleend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="singleend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/>
+                </repeat>
+            </repeat>
+            <param name="report" type="boolean" value="False"/>
+            <param name="fdr_cutoff" value="0.05"/>
+            <output name="dexseq_out" file="DEXSeq_result_file.tabular" ftype="tabular"/>
+        </test>
+    </tests>
     <help>
 
 .. class:: infomark