# HG changeset patch
# User bgruening
# Date 1561279220 14400
# Node ID 67049a07122678091ed579c70dc8bd6a7c9a108e
# Parent  c63b6a7c7b7e9cc26b31973100bcb52307fc2eb7
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189

diff -r c63b6a7c7b7e -r 67049a071226 nanopolish_eventalign.xml
--- a/nanopolish_eventalign.xml	Tue Jun 18 12:31:29 2019 -0400
+++ b/nanopolish_eventalign.xml	Sun Jun 23 04:40:20 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="0.1.0">
+<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="0.11.1">
     <description>- Align nanopore events to reference k-mers</description>
     <macros>
         <import>macros.xml</import>
@@ -67,7 +67,7 @@
     <inputs>
       <!-- index inputs -->
         <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/>
-        <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
+        <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>
 
         <!-- variants consensus inputs -->
         <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" />
@@ -161,8 +161,8 @@
             <param name="input_merged" ftype="fasta" value="reads.fasta" />
             <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" />
             <param name="b" value="reads.sorted.bam" />
-            <param name="reference_source_selector" value="cached" />
-            <param name="ref_file" value="draft"/>
+            <param name="reference_source_selector" value="history" />
+            <param name="ref_file" value="draft.fa"/>
             <param name="w" value="tig00000001:200000-200010" />
             <param name="sam" value="false" />
             <param name="summary" value="false" />
diff -r c63b6a7c7b7e -r 67049a071226 test-data/all_fasta.loc
--- a/test-data/all_fasta.loc	Tue Jun 18 12:31:29 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-draft	draft	draft	${__HERE__}/draft.fa
\ No newline at end of file
diff -r c63b6a7c7b7e -r 67049a071226 test-data/all_fasta.loc.sample
--- a/test-data/all_fasta.loc.sample	Tue Jun 18 12:31:29 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-draft	draft	draft	${__HERE__}/draft.fa
\ No newline at end of file
diff -r c63b6a7c7b7e -r 67049a071226 test-data/all_fasta.loc.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc.test	Sun Jun 23 04:40:20 2019 -0400
@@ -0,0 +1,1 @@
+draft	draft	draft	${__HERE__}/draft.fa
\ No newline at end of file
diff -r c63b6a7c7b7e -r 67049a071226 tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Tue Jun 18 12:31:29 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>	<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#
-