# HG changeset patch
# User artbio
# Date 1591535286 14400
# Node ID 6a69e5d7c21fc0f494955951ad223a4bc53724d8
# Parent  c35d9902100e40aa18833f616b288dd1e24871a7
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 0c076cce96ddede06511d9fb8ebc707b9f083a1d"

diff -r c35d9902100e -r 6a69e5d7c21f manta_macros.xml
--- a/manta_macros.xml	Wed May 13 15:42:33 2020 -0400
+++ b/manta_macros.xml	Sun Jun 07 09:08:06 2020 -0400
@@ -1,7 +1,7 @@
 <macros>
 
     <token name="@VERSION@">1.6</token>
-    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy3</token>
+    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy4</token>
     <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
 
     <token name="@set_reference_fasta_filename@"><![CDATA[
@@ -51,7 +51,7 @@
             </param>
             <when value="cached">
                 <param name="index" type="select" label="Using reference genome" help="Select genome from the list">
-                    <options from_data_table="all_fasta">
+                    <options from_data_table="fasta_indexes">
                         <filter type="sort_by" column="2" />
                         <validator type="no_options" message="No indexes are available" />
                     </options>
diff -r c35d9902100e -r 6a69e5d7c21f test-data/all_fasta.loc
--- a/test-data/all_fasta.loc	Wed May 13 15:42:33 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +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). 
-This file has the format (white space characters are TAB characters):
-#
-#<unique_build_id>      <dbkey>         <display_name>  <file_path>
-#
-#So, it could look something like this:
-#
-#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 .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.
-hg19	hg19	Human hg19	${__HERE__}/cached_locally/cached_region.fa
diff -r c35d9902100e -r 6a69e5d7c21f test-data/cached_locally/all_fasta.loc
--- a/test-data/cached_locally/all_fasta.loc	Wed May 13 15:42:33 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-hg19	hg19	Human hg19	${__HERE__}/cached_region.fa
diff -r c35d9902100e -r 6a69e5d7c21f test-data/cached_locally/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/fasta_indexes.loc	Sun Jun 07 09:08:06 2020 -0400
@@ -0,0 +1,1 @@
+hg19	hg19	Human hg19	${__HERE__}/cached_region.fa
diff -r c35d9902100e -r 6a69e5d7c21f test-data/candidateSV.vcf.gz
Binary file test-data/candidateSV.vcf.gz has changed
diff -r c35d9902100e -r 6a69e5d7c21f test-data/candidateSmallIndels.vcf.gz
Binary file test-data/candidateSmallIndels.vcf.gz has changed
diff -r c35d9902100e -r 6a69e5d7c21f test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Sun Jun 07 09:08:06 2020 -0400
@@ -0,0 +1,31 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/sam_indexes/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/path/to/genome/hg18/sam_indexes/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/path/to/genome/sam_indexes/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/sam_indexes/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/sam_indexes/hg19full.fa
+
+hg19	hg19	Human hg19	${__HERE__}/cached_locally/cached_region.fa
diff -r c35d9902100e -r 6a69e5d7c21f tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Wed May 13 15:42:33 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +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). 
-This file has the format (white space characters are TAB characters):
-#
-#<unique_build_id>      <dbkey>         <display_name>  <file_path>
-#
-#So, it could look something like this:
-#
-#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 .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.
diff -r c35d9902100e -r 6a69e5d7c21f tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Sun Jun 07 09:08:06 2020 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/sam_indexes/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/path/to/genome/hg18/sam_indexes/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/path/to/genome/sam_indexes/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/sam_indexes/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/sam_indexes/hg19full.fa
\ No newline at end of file
diff -r c35d9902100e -r 6a69e5d7c21f tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed May 13 15:42:33 2020 -0400
+++ b/tool_data_table_conf.xml.sample	Sun Jun 07 09:08:06 2020 -0400
@@ -1,6 +1,6 @@
 <tables>
-    <table name="all_fasta" comment_char="#">
+    <table name="fasta_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="${__HERE__}/test-data/all_fasta.loc" />
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
     </table>
 </tables>