# HG changeset patch
# User mvdbeek
# Date 1485522624 18000
# Node ID 540a84c471e9f5de038c35548e464faf10e5227e
# Parent  ff6683f8e9a1fe12b421e7efe16b225e38673d2f
planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7-dirty

diff -r ff6683f8e9a1 -r 540a84c471e9 tepid_merge_deletions.xml
--- a/tepid_merge_deletions.xml	Mon Jan 23 10:05:02 2017 -0500
+++ b/tepid_merge_deletions.xml	Fri Jan 27 08:10:24 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="tepid_merge_deletions" name="tepid-merge-deletions" version="@WRAPPER_VERSION@">
+<tool id="tepid_merge_deletions" name="tepid-merge-deletions" version="@WRAPPER_VERSION@.1">
     <description>merge discovered TE deletions</description>
     <macros>
         <import>macros.xml</import>
@@ -13,22 +13,22 @@
         #for $input in $deletions:
             '$input.element_identifier'
         #end for
-        -o merged.bed && cat merged.bed && python $__tool_directory__/flip_deletions.py
+        -o '$merged_out' python $__tool_directory__/flip_deletions.py
         -s
         #for $sample in $deletions:
             '$sample.element_identifier'
         #end for
-        -d merged.bed
+        -d '$merged_out'
         -r '$reference_name'
-        -o '$merged_out'
+        -o '$merged_flipped_out'
     ]]></command>
     <inputs>
         <param name="deletions" label="TEPID deletions" argument="--input" type="data_collection" collection_type="list" format="bed"/>
         <param name="reference_name" label="Reference sample name" argument="--reference" type="text" value="ref"/>
     </inputs>
     <outputs>
-        <data name="merged_out" format="bed" label="tepid_discover merged deletions on ${on_string}">
-        </data>
+        <data name="merged_out" format="bed" label="tepid_discover merged deletions on ${on_string}"/>
+        <data name="merged_flipped_out" format="bed" label="tepid_discover merged and flipped deletions on ${on_string}"/>
     </outputs>
     <tests>
         <test>