# HG changeset patch
# User iuc
# Date 1768849631 0
# Node ID ec790193c2f291e8dd345cb698d25a53692c725f
# Parent  8a48a407e50ca0f52f65546806c9e7d6af0f0fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit 747e3f71fa11ce2555debdb5fdb6dce9838c71af

diff -r 8a48a407e50c -r ec790193c2f2 tool-data/lastz_seqs.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/lastz_seqs.loc.sample	Mon Jan 19 19:07:11 2026 +0000
@@ -0,0 +1,30 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of 2bit genome files for use with Lastz. You will
+#need to supply these files and then create a lastz_seqs.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The lastz_seqs.loc
+#file has this format (white space characters are TAB characters):
+#
+#<unique_build_id>	<display_name>		<file_path>
+#
+#So, for example, if your lastz_seqs.loc began like this:
+#
+#hg18	Human (Homo sapiens): hg18		/depot/data2/galaxy/twobit/hg18.2bit
+#hg19	Human (Homo sapiens): hg19		/depot/data2/galaxy/twobit/hg19.2bit
+#mm9	Mouse (Mus musculus): mm9		/depot/data2/galaxy/twobit/mm9.2bit
+#
+#then your /depot/data2/galaxy/twobit/ directory
+#would need to contain the following 2bit files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.2bit
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg19.2bit
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 mm9.2bit
+#
+#Your lastz_seqs.loc file should include an entry per line for 
+#each file you have stored that you want to be available. Note that 
+#your files should all have the extension '2bit'.
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. 
+#
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diff -r 8a48a407e50c -r ec790193c2f2 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Jan 19 19:07:11 2026 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of 2bit sequence files for use in Lastz -->
+    <table name="lastz_seqs" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/lastz_seqs.loc" />
+    </table>
+</tables>
\ No newline at end of file
diff -r 8a48a407e50c -r ec790193c2f2 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Jan 19 19:07:11 2026 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of 2bit sequence files for use in Lastz -->
+    <table name="lastz_seqs" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/lastz_seqs.loc" />
+    </table>
+</tables>
\ No newline at end of file