# HG changeset patch
# User iuc
# Date 1443212799 14400
# Node ID a26a82bed63f360fc4d1e794288627daf82a1283
# Parent  b19cb9385f288bc84430e882f4d847ec101a30a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96

diff -r b19cb9385f28 -r a26a82bed63f dexseq.xml
--- 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"/>
diff -r b19cb9385f28 -r a26a82bed63f dexseq_count.xml
--- a/dexseq_count.xml	Fri Sep 25 15:57:00 2015 -0400
+++ b/dexseq_count.xml	Fri Sep 25 16:26:39 2015 -0400
@@ -1,11 +1,18 @@
 <tool id="dexseq_count" name="DEXSeq-Count" version="1.0">
     <description>Prepare and count exon abundancies from RNA-seq data</description>
     <requirements>
-        <requirement type="package" version="3.1.0">R</requirement>
-        <requirement type="package" version="1.14.2">dexseq</requirement>
+        <requirement type="package" version="1.14">dexseq</requirement>
         <requirement type="package" version="0.6.1">htseq</requirement>
-        <requirement type="package" version="0.7.6">pysam</requirement>
+        <requirement type="package" version="0.7.7">pysam</requirement>
     </requirements>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <command>
     <![CDATA[
         #if $mode.mode_select == "prepare":
@@ -26,14 +33,6 @@
         #end if
     ]]>
     </command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <!-- In case the return code has not been set propery check stderr too -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
     <inputs>
         <conditional name="mode">
             <param name="mode_select" type="select" label="Mode of operation">
@@ -66,10 +65,10 @@
 
     <outputs>
         <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}">
-            <filter>(mode['mode_select'] == 'count')</filter>
+            <filter>mode['mode_select'] == 'count'</filter>
         </data>
-        <data format="gff" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}">
-            <filter>(mode['mode_select'] == 'prepare')</filter>
+        <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}">
+            <filter>mode['mode_select'] == 'prepare'</filter>
         </data>
     </outputs>
 
diff -r b19cb9385f28 -r a26a82bed63f tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 25 15:57:00 2015 -0400
+++ b/tool_dependencies.xml	Fri Sep 25 16:26:39 2015 -0400
@@ -1,5 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="pysam" version="0.7.7">
+        <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="htseq" version="0.6.1">
+        <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" />
     </package>