diff dexseq.xml @ 3:a26a82bed63f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96

--- a/dexseq.xml	Fri Sep 25 15:57:00 2015 -0400
+++ b/dexseq.xml	Fri Sep 25 16:26:39 2015 -0400
@@ -4,6 +4,20 @@
         <requirement type="package" version="1.14">dexseq</requirement>
     </requirements>
     <code file="dexseq_helper.py" />
+    <stdio>
+        <regex match="Execution halted" 
+           source="both" 
+           level="fatal" 
+           description="Execution halted." />
+        <regex match="Input-Error 01" 
+           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" 
+           description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
     <command>
     <![CDATA[
         mkdir ./html_out &&
@@ -38,22 +52,8 @@
         &&
     ]]>
     </command>
-    <stdio>
-        <regex match="Execution halted" 
-           source="both" 
-           level="fatal" 
-           description="Execution halted." />
-        <regex match="Input-Error 01" 
-           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" 
-           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" format="gtf,gff" 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">
@@ -68,7 +68,7 @@
                         <valid initial="string.letters,string.digits"><add value="_" /></valid>
                     </sanitizer>
                 </param>
-                <param name="countsFile" type="data" multiple="true" label="Counts file"/>
+                <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/>
             </repeat>
         </repeat>
         <param name="report" type="boolean" truevalue="" falsevalue="" checked="true"
@@ -76,15 +76,12 @@
             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."/>
     </inputs>
-
     <outputs>
         <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>
         </data>
     </outputs>
-    
-    <code file="dexseq_helper.py" />
     <tests>
         <test>
             <param name="gtf" value="dexseq.gtf" ftype="bed"/>