# HG changeset patch
# User iuc
# Date 1443377188 14400
# Node ID 7069d55968fbe91790d75a5735f0512b81348d64
# Parent  a26a82bed63f360fc4d1e794288627daf82a1283
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit f06ef03a7394f5be6fab607283f6d100c2a9a267

diff -r a26a82bed63f -r 7069d55968fb dexseq.xml
--- a/dexseq.xml	Fri Sep 25 16:26:39 2015 -0400
+++ b/dexseq.xml	Sun Sep 27 14:06:28 2015 -0400
@@ -13,9 +13,9 @@
            source="both" 
            level="fatal" 
            description="Error in your input parameters: Make sure you only apply factors to selected samples." />
-        <regex match="Error in" 
-           source="both" 
-           level="fatal" 
+        <regex match="Error in"
+           source="both"
+           level="fatal"
            description="An undefined error occured, please check your intput carefully and contact your administrator." />
     </stdio>
     <command>
@@ -39,17 +39,18 @@
             #end for
             -f '#echo json.dumps(temp_factor_names)#'
             -a $gtf
+            -c $fdr_cutoff
+
             #if $report:
                 -r ./html_out
+                &&
+                mkdir $htmlreport.extra_files_path
+                &&
+                cp ./html_out/testForDEU.html $htmlreport
+                &&
+                cp -r ./html_out/* $htmlreport.extra_files_path
             #end if
-            -c $fdr_cutoff
-        &&
-        mkdir $htmlreport.extra_files_path
-        &&
-        cp ./html_out/testForDEU.html $htmlreport
-        &&
-        cp -r ./html_out/* $htmlreport.extra_files_path
-        &&
+
     ]]>
     </command>
     <inputs>
@@ -71,83 +72,43 @@
                 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/>
             </repeat>
         </repeat>
-        <param name="report" type="boolean" truevalue="" falsevalue="" checked="true"
+        <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
             label="Visualise the analysis results?"
-            help="output an additional html file" />
-        <param name="fdr_cutoff" type="float" min="0" max="1" value="0.05" label="All the genes under this FDR threshold will be shown in the html report."/>
+            help="Output an additional HTML file." />
+        <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/>
+        <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" />
         <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}">
-            <filter>report == True</filter>
+            <filter>report is True</filter>
         </data>
     </outputs>
     <tests>
         <test>
             <param name="gtf" value="dexseq.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>
+                <param name="factorName" value="condition"/>
                 <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"/>
+                    <param name="factorLevel" value="knockdown"/>
+                    <param name="countsFile" value="treated1fb.txt,treated2fb.txt,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"/>
+                    <param name="factorLevel" value="control"/>
+                    <param name="countsFile" value="untreated1fb.txt,untreated2fb.txt,untreated2fb.txt,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>
+                <param name="factorName" value="libtype"/>
                 <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"/>
+                    <param name="factorLevel" value="singleend"/>
+                    <param name="countsFile" ftype="tabular" value="treated1fb.txt,untreated1fb.txt,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"/>
+                    <param name="factorLevel" value="pairedend"/>
+                    <param name="countsFile" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt"/>
                 </repeat>
             </repeat>
-            <param name="report" type="boolean" value="False"/>
+            <param name="report" value="False"/>
             <param name="fdr_cutoff" value="0.05"/>
             <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/>
         </test>
diff -r a26a82bed63f -r 7069d55968fb tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 25 16:26:39 2015 -0400
+++ b/tool_dependencies.xml	Sun Sep 27 14:06:28 2015 -0400
@@ -7,6 +7,6 @@
         <repository changeset_revision="025da27a2bb2" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="dexseq" version="1.14">
-       <repository changeset_revision="cb7ad0ece9e8" name="package_dexseq_1_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="d8a45cbc4208" name="package_dexseq_1_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>