# HG changeset patch
# User sanbi-uwc
# Date 1551965082 18000
# Node ID 3892ea8ad1ad44caf7c42f27866fb8139dd2cec4
# Parent  96c8c5cada4786f4e56a58c68a19484ef61ba5cf
planemo upload for repository https://github.com/COMBAT-TB/confil commit 371cae3aab4e4874410d5bcdc7885908ce765181

diff -r 96c8c5cada47 -r 3892ea8ad1ad conda/conda_upload.sh
--- a/conda/conda_upload.sh	Thu Mar 07 07:12:34 2019 -0500
+++ b/conda/conda_upload.sh	Thu Mar 07 08:24:42 2019 -0500
@@ -2,12 +2,9 @@
 # Only need to change these two variables
 PKG_NAME=confil
 USER=thoba
-
 OS=$TRAVIS_OS_NAME-64
 
 conda config --set anaconda_upload no
-DEV='dev'
-DATE=`date +%Y%m%d`
 export CONDA_BLD_PATH=$HOME/miniconda/conda-bld
 conda build .
 anaconda -t $CONDA_UPLOAD_TOKEN upload -u $USER $CONDA_BLD_PATH/$OS/$PKG_NAME-*.tar.bz2 --force
diff -r 96c8c5cada47 -r 3892ea8ad1ad confil.egg-info/PKG-INFO
--- a/confil.egg-info/PKG-INFO	Thu Mar 07 07:12:34 2019 -0500
+++ b/confil.egg-info/PKG-INFO	Thu Mar 07 08:24:42 2019 -0500
@@ -1,9 +1,12 @@
-Metadata-Version: 2.1
+Metadata-Version: 1.0
 Name: confil
-Version: 0.1.3.dev20190307
+Version: 0.1.2.dev20190304
 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)
@@ -33,4 +36,3 @@
         
 Keywords: contamination,filter
 Platform: UNKNOWN
-Description-Content-Type: text/markdown
diff -r 96c8c5cada47 -r 3892ea8ad1ad confil.egg-info/SOURCES.txt
--- a/confil.egg-info/SOURCES.txt	Thu Mar 07 07:12:34 2019 -0500
+++ b/confil.egg-info/SOURCES.txt	Thu Mar 07 08:24:42 2019 -0500
@@ -3,10 +3,13 @@
 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 96c8c5cada47 -r 3892ea8ad1ad confil.xml
--- a/confil.xml	Thu Mar 07 07:12:34 2019 -0500
+++ b/confil.xml	Thu Mar 07 08:24:42 2019 -0500
@@ -1,21 +1,24 @@
-<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy0">
+<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy1">
     <macros>
-	<token name="@VERSION@">0.1.3</token>
+        <token name="@VERSION@">0.1.3</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">confil</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        ln -s \$(which kraken2) \$(pwd)/kraken2 && 
+        PATH=\$(pwd):\$PATH && export PATH &&
+
         #set $input_type = $input_type_conditional.input_type
         #import re
-
+        
         ####### Single Input
         #if $input_type == "single"
         ln -s "${input_type_conditional.single_input}" $input_type_conditional.single_input.element_identifier &&
         #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0]
         #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab'
 
-        confil --threads $threads --cutoff $cutoff 
+        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'
@@ -27,7 +30,7 @@
         #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 $threads --cutoff $cutoff --paired 
+        confil --threads \${GALAXY_SLOTS:-1} --cutoff $cutoff --paired 
         $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier
         && mv $report_name '$output_report'
         && ln -sf "${input_type_conditional.collection_input.forward}" '$list_output.forward'
@@ -48,8 +51,7 @@
                 <param name="collection_input" format="fq,fastq,fastq.gz,fastqsanger" type="data_collection" collection_type="paired" label="Select Dataset Pair" help="Specify paired dataset collection containing paired reads" />
             </when>
         </conditional>
-        <param name="cutoff" type="integer" label="Cutoff percentage" value="50" min="50" max="99" />
-        <param name="threads" type="integer" label="Number of threads" value="1" min="1" max="4" />
+        <param name="cutoff" type="integer" label="Cutoff percentage" value="90" min="50" max="99" />
     </inputs>
     <outputs>
         <data name="output_report" format="tabular" label="Kraken2 report" />
diff -r 96c8c5cada47 -r 3892ea8ad1ad confil/__init__.pyc
Binary file confil/__init__.pyc has changed
diff -r 96c8c5cada47 -r 3892ea8ad1ad confil/confil.pyc
Binary file confil/confil.pyc has changed
diff -r 96c8c5cada47 -r 3892ea8ad1ad confil/kraken.pyc
Binary file confil/kraken.pyc has changed
diff -r 96c8c5cada47 -r 3892ea8ad1ad confil/report.pyc
Binary file confil/report.pyc has changed