# HG changeset patch
# User bgruening
# Date 1620370166 0
# Node ID 855b7ba0ce9ce0feabb6ca84c8f6d39240cef003
# Parent  8fdb079ddaf076c212e41500d30f01792389fb61
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4883f9a9a2779e2b4792314bd6128c7c109c00e1"

diff -r 8fdb079ddaf0 -r 855b7ba0ce9c nanopolish_eventalign.xml
--- a/nanopolish_eventalign.xml	Fri May 29 13:29:43 2020 -0400
+++ b/nanopolish_eventalign.xml	Fri May 07 06:49:26 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy0">
+<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy1">
     <description>- Align nanopore events to reference k-mers</description>
     <macros>
         <import>macros.xml</import>
@@ -49,6 +49,7 @@
         --threads "\${GALAXY_SLOTS:-4}"        
         $samples
         $scale_events
+        $signal_index
         $sam
         $print_read_names
         #if $w and str($w).strip():
@@ -110,6 +111,10 @@
             label="Write the raw samples for the event to the tsv output" />
         <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false"
             label="Scale events to the model, rather than vice-versa" />
+        <param name="signal_index" argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false"
+            label="write the raw signal start and end index values for the event to the tsv output" />
+
+
         <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false"
             label="write output in SAM format" />
         <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false"
diff -r 8fdb079ddaf0 -r 855b7ba0ce9c test-data/all_fasta.loc
--- a/test-data/all_fasta.loc	Fri May 29 13:29:43 2020 -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 8fdb079ddaf0 -r 855b7ba0ce9c test-data/all_fasta.loc.sample
--- a/test-data/all_fasta.loc.sample	Fri May 29 13:29:43 2020 -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 8fdb079ddaf0 -r 855b7ba0ce9c tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Fri May 29 13:29:43 2020 -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.
-#
-