# HG changeset patch
# User sanbi-uwc
# Date 1552067183 18000
# Node ID 2cde7c81c694f14790581189d2a1d6678a58da9e
# Parent  3365813ad7f5d6e136da495e0bacd25c3e73cd05
planemo upload for repository https://github.com/COMBAT-TB/confil commit 036172521321dbafe62e6d72b3a491f4bc4b9dc9-dirty

diff -r 3365813ad7f5 -r 2cde7c81c694 confil.egg-info/PKG-INFO
--- a/confil.egg-info/PKG-INFO	Fri Mar 08 02:27:28 2019 -0500
+++ b/confil.egg-info/PKG-INFO	Fri Mar 08 12:46:23 2019 -0500
@@ -1,12 +1,9 @@
-Metadata-Version: 1.0
+Metadata-Version: 2.1
 Name: confil
-Version: 0.1.2.dev20190304
+Version: 0.1.3.dev20190307
 Summary: Contamination filter
 Home-page: https://github.com/COMBAT-TB/confil
-Author: UNKNOWN
-Author-email: UNKNOWN
 License: UNKNOWN
-Description-Content-Type: text/markdown
 Description: # confil
         
         [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil)
@@ -36,3 +33,4 @@
         
 Keywords: contamination,filter
 Platform: UNKNOWN
+Description-Content-Type: text/markdown
diff -r 3365813ad7f5 -r 2cde7c81c694 confil.egg-info/SOURCES.txt
--- a/confil.egg-info/SOURCES.txt	Fri Mar 08 02:27:28 2019 -0500
+++ b/confil.egg-info/SOURCES.txt	Fri Mar 08 12:46:23 2019 -0500
@@ -3,13 +3,10 @@
 setup.py
 confil/__init__.py
 confil/confil.py
-confil/kraken.py
-confil/report.py
 confil.egg-info/PKG-INFO
 confil.egg-info/SOURCES.txt
 confil.egg-info/dependency_links.txt
 confil.egg-info/entry_points.txt
 confil.egg-info/requires.txt
 confil.egg-info/top_level.txt
-test/test_report.py
 test/test_runner.py
\ No newline at end of file
diff -r 3365813ad7f5 -r 2cde7c81c694 confil.xml
--- a/confil.xml	Fri Mar 08 02:27:28 2019 -0500
+++ b/confil.xml	Fri Mar 08 12:46:23 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy2">
+<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy3">
     <macros>
         <token name="@VERSION@">0.1.3</token>
     </macros>
@@ -16,11 +16,13 @@
         #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0]
         #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab'
 
-        confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff 
-        $input_type_conditional.single_input.element_identifier
-        && mv $report_name '$output_report'
-        && ln -sf "${input_type_conditional.single_input}" '$single_output_file'
-
+        if confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff 
+          $input_type_conditional.single_input.element_identifier ;
+        then 
+          ln -sf "${input_type_conditional.single_input}" '$single_output_file'
+	else
+	  touch '$single_output_file'  # failure - make empty file
+	fi
         ####### Paired Collection
         #elif $input_type == "paired_collection"
         ln -s "${input_type_conditional.collection_input.forward}" $input_type_conditional.collection_input.forward.element_identifier &&
@@ -28,12 +30,16 @@
         #set report_name = os.path.splitext(os.path.basename($input_type_conditional.collection_input.forward.element_identifier))[0]
         #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab'
 
-        confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff --paired 
-        $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier
+        if confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff --paired 
+        $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier ;
+	then 
+          ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward'
+          && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse'
+	else
+	  touch '$list_output.forward' && touch '$list_output.reverse'  # failure - make empty files
+	fi
+        #end if
         && mv $report_name '$output_report'
-        && ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward'
-        && ln -sf "${input_type_conditional.collection_input.reverse}" '$list_output.reverse'
-        #end if
     ]]>
     </command>
     <inputs>
diff -r 3365813ad7f5 -r 2cde7c81c694 confil/.confil.py.swp
Binary file confil/.confil.py.swp has changed
diff -r 3365813ad7f5 -r 2cde7c81c694 confil/__init__.pyc
Binary file confil/__init__.pyc has changed
diff -r 3365813ad7f5 -r 2cde7c81c694 confil/confil.pyc
Binary file confil/confil.pyc has changed
diff -r 3365813ad7f5 -r 2cde7c81c694 confil/kraken.pyc
Binary file confil/kraken.pyc has changed
diff -r 3365813ad7f5 -r 2cde7c81c694 confil/report.pyc
Binary file confil/report.pyc has changed