# HG changeset patch
# User pavanvidem
# Date 1441293968 14400
# Node ID 45022897fb7d0c43e20b896dc22c8ea5df20ef1c
# Parent  169c48f14f3155221dc179d18310e5c3ebabc195
Uploaded

diff -r 169c48f14f31 -r 45022897fb7d dexseq_count.xml
--- a/dexseq_count.xml	Thu Sep 03 05:40:06 2015 -0400
+++ b/dexseq_count.xml	Thu Sep 03 11:26:08 2015 -0400
@@ -4,11 +4,11 @@
         <requirement type="package" version="3.1.0">R</requirement>
         <requirement type="package" version="1.14.2">DEXSeq</requirement> 
     </requirements>
-    <command>
+    <command interpreter="python">
         #if $mode.mode_select == "prepare":
-            python $INSTALL_DIR/python_scripts/dexseq_prepare_annotation.py -r $aggregate $gtf $flattened_gtf_out
+            dexseq_prepare_annotation.py -r $aggregate $gtffile $flattened_gtf_out
         #elif $mode.mode_select == "count":
-            python $INSTALL_DIR/python_scripts/dexseq_count.py -f bam -p $paired -r $order -s $stranded $flattened_gtf_in $bamfile $counts_file
+            dexseq_count.py -f bam -p $paired -r $order -s $stranded $flattened_gtf_in $bamfile $counts_file
         #end if
     </command>
     <inputs>
@@ -18,19 +18,19 @@
                 <option value="count">Count reads</option>
             </param>
             <when value="prepare">
-                <param name="gtf" type="gtf" label="GTF file"/>
+                <param name="gtffile" type="data" format="gff" label="GTF file"/>
                 <param name="aggregate" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Aggretare genes with  exons?" help="Indicates whether two or more genes sharing an exon should be merged into an 'aggregate gene'. If 'no', the exons that can not be assiged to a single gene are ignored."/>
             </when>
             <when value="count">
-                <param name="bamfile" type="bam" label="Input bam file"/>
-                <param name="flattened_gtf_in" type="gtf" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
-                <param name="paired" type="boolean" checked="False" truevalue="yes" falsevalue="no" label="Is libray paired end?"/>
+                <param name="bamfile" type="data" format="bam" label="Input bam file"/>
+                <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/>
+                <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/>
                 <param name="stranded" type="select" label="Is library strand specific?">
                     <option value="no">No</option>
                     <option value="yes">Yes</option>
                     <option value="reverse">Yes, but reverse</option>
                 </param>
-                <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value">
+                <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/>
                 <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data">
                     <option value="pos">By position</option>
                     <option value="name">By name</option>
@@ -43,7 +43,7 @@
         <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}">
             <filter>(mode['mode_select'] == 'count')</filter>
         </data>
-        <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}">
+        <data format="gff" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}">
             <filter>(mode['mode_select'] == 'prepare')</filter>
         </data>
     </outputs>
diff -r 169c48f14f31 -r 45022897fb7d tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Sep 03 05:40:06 2015 -0400
+++ b/tool_dependencies.xml	Thu Sep 03 11:26:08 2015 -0400
@@ -80,6 +80,9 @@
                     <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/statmod_1.4.21.tar.gz</package>
                     <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/DEXSeq_1.14.2.tar.gz</package>
                 </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/DEXSeq/python_scripts/</environment_variable>
+                </action>
             </actions>
         </install>
         <readme>