# HG changeset patch
# User fubar
# Date 1720929415 0
# Node ID d3019082500238a33c68f9c15aced6bea54de941
# Parent  e2e1e48a2e56f00bea890968dd5dade77f6ab110
planemo upload for repository https://github.com/fubar2/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty

diff -r e2e1e48a2e56 -r d30190825002 README.md
--- a/README.md	Sun Jul 14 02:22:32 2024 +0000
+++ b/README.md	Sun Jul 14 03:56:55 2024 +0000
@@ -1,5 +1,6 @@
 ## microsatellites to bed features
 
+
  **Convert short repetitive sequences to bed features**
 
  Microsatellites refer to short DNA patterns that are repeated.
diff -r e2e1e48a2e56 -r d30190825002 all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Sun Jul 14 03:56:55 2024 +0000
@@ -0,0 +1,18 @@
+#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.
+#
diff -r e2e1e48a2e56 -r d30190825002 microsatbed.xml
--- a/microsatbed.xml	Sun Jul 14 02:22:32 2024 +0000
+++ b/microsatbed.xml	Sun Jul 14 03:56:55 2024 +0000
@@ -1,4 +1,4 @@
-<tool name="STR to bed" id="microsatbedfubar" version="1.3.0" profile="22.05">
+<tool name="strtobed" id="microsatbedfubar" version="1.3.0" profile="22.05">
   <description>Short Tandem Repeats to bed features from fasta</description>
   <requirements>
     <requirement version="3.12.3" type="package">python</requirement>
diff -r e2e1e48a2e56 -r d30190825002 test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Sun Jul 14 03:56:55 2024 +0000
@@ -0,0 +1,22 @@
+#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.
+#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.
+#
+hgtest	hgtest	hgtest	${__HERE__}/humsamp.fa
diff -r e2e1e48a2e56 -r d30190825002 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sun Jul 14 02:22:32 2024 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Jul 14 03:56:55 2024 +0000
@@ -2,6 +2,6 @@
     <!-- Locations of all fasta files under genome directory -->
     <table name="all_fasta" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc.sample" />
+        <file path="test-data/all_fasta.loc" />
     </table>
 </tables>
diff -r e2e1e48a2e56 -r d30190825002 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test	Sun Jul 14 02:22:32 2024 +0000
+++ b/tool_data_table_conf.xml.test	Sun Jul 14 03:56:55 2024 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Locations of dbkeys and len files under genome directory -->
-    <table name="__dbkeys__" comment_char="#" allow_duplicate_entries="False">
+    <table name="all_fasta" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="${__HERE__}/tool-data/all_fasta.loc.sample" />
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
     </table>
 </tables>