# HG changeset patch
# User iuc
# Date 1592414907 14400
# Node ID 25abc2c72ff96fb3ccf984cb97d9c0192b563456
# Parent  c43f4b80f5a930cb62433df7a21ec5bb4dc76d56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit a57b5b935a80db12a0ed867b4219453a2854dd32"

diff -r c43f4b80f5a9 -r 25abc2c72ff9 NanocomporeDB_process.py
--- a/NanocomporeDB_process.py	Mon Jun 08 14:36:18 2020 -0400
+++ b/NanocomporeDB_process.py	Wed Jun 17 13:28:27 2020 -0400
@@ -38,7 +38,7 @@
     parser.add_argument('--pvalue-types', type=str,
                         default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue',
                         help='path to the annotations')
-    parser.add_argument('--bedgraph', default=False,
+    parser.add_argument('--bedgraph', action="store_true",
                         help='write output in BEDGRAPH format instead of BED')
     parser.add_argument('--pvalue-threshold', default=1.0,
                         help='Maximum reported p-value.')
diff -r c43f4b80f5a9 -r 25abc2c72ff9 macros.xml
--- a/macros.xml	Mon Jun 08 14:36:18 2020 -0400
+++ b/macros.xml	Wed Jun 17 13:28:27 2020 -0400
@@ -1,7 +1,6 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.0.0rc3.post2</token>
-    <token name="@WRAPPER_VERSION@">galaxy0</token>
     <token name="@DESCRIPTION@"></token>
     <xml name="requirements">
         <requirements>
@@ -29,4 +28,4 @@
     <token name="@REFERENCES@"><![CDATA[
 More information are available on the `project website <https://nanocompore.rna.rocks/>`_ and `github <https://github.com/tleonardi/nanocompore>`_.
     ]]></token>
-</macros>
\ No newline at end of file
+</macros>
diff -r c43f4b80f5a9 -r 25abc2c72ff9 sampcomp.xml
--- a/sampcomp.xml	Mon Jun 08 14:36:18 2020 -0400
+++ b/sampcomp.xml	Wed Jun 17 13:28:27 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
+<tool id="nanocompore_sampcomp" name="SampComp" version="@TOOL_VERSION@+galaxy0">
     <description>to compare Nanopolished datasets</description>
     <macros>
         <import>macros.xml</import>
@@ -217,4 +217,4 @@
 @REFERENCES@
     ]]></help>
     <expand macro="citations"/>
-</tool>
\ No newline at end of file
+</tool>
diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/GMM_logit_pvalue.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GMM_logit_pvalue.bed	Wed Jun 17 13:28:27 2020 -0400
@@ -0,0 +1,2 @@
+chr	22102	22107	chr_AGGAA	0	+
+chr	22103	22108	chr_GGAAA	1.0472150418546853	+
diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/GMM_logit_pvalue.bedgraph
--- a/test-data/GMM_logit_pvalue.bedgraph	Mon Jun 08 14:36:18 2020 -0400
+++ b/test-data/GMM_logit_pvalue.bedgraph	Wed Jun 17 13:28:27 2020 -0400
@@ -1,2 +1,2 @@
-chr	22102	22107	chr_AGGAA	0	+
-chr	22103	22108	chr_GGAAA	1.0472150418546853	+
+chr	22104	22105	0
+chr	22105	22106	1.0472150418546853
diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_dwell_pvalue.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/KS_dwell_pvalue.bed	Wed Jun 17 13:28:27 2020 -0400
@@ -0,0 +1,2 @@
+chr	22102	22107	chr_AGGAA	0.037294307603991536	+
+chr	22103	22108	chr_GGAAA	0.037294307603991536	+
diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_dwell_pvalue.bedgraph
--- a/test-data/KS_dwell_pvalue.bedgraph	Mon Jun 08 14:36:18 2020 -0400
+++ b/test-data/KS_dwell_pvalue.bedgraph	Wed Jun 17 13:28:27 2020 -0400
@@ -1,2 +1,2 @@
-chr	22102	22107	chr_AGGAA	0.037294307603991536	+
-chr	22103	22108	chr_GGAAA	0.037294307603991536	+
+chr	22104	22105	0.037294307603991536
+chr	22105	22106	0.037294307603991536
diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_intensity_pvalue.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/KS_intensity_pvalue.bed	Wed Jun 17 13:28:27 2020 -0400
@@ -0,0 +1,2 @@
+chr	22102	22107	chr_AGGAA	0.5940708247528699	+
+chr	22103	22108	chr_GGAAA	0.5940708247528699	+
diff -r c43f4b80f5a9 -r 25abc2c72ff9 test-data/KS_intensity_pvalue.bedgraph
--- a/test-data/KS_intensity_pvalue.bedgraph	Mon Jun 08 14:36:18 2020 -0400
+++ b/test-data/KS_intensity_pvalue.bedgraph	Wed Jun 17 13:28:27 2020 -0400
@@ -1,2 +1,2 @@
-chr	22102	22107	chr_AGGAA	0.5940708247528699	+
-chr	22103	22108	chr_GGAAA	0.5940708247528699	+
+chr	22104	22105	0.5940708247528699
+chr	22105	22106	0.5940708247528699