# HG changeset patch
# User iuc
# Date 1518184786 18000
# Node ID da6d7bc0a8b0b7b82d4cfa6c539b5698796c35a7
# Parent  3f852f713d2472687c874c0b443d03a67c82ffa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6418f2e58def1a81b3aa7c04cb5dc33decea1a96

diff -r 3f852f713d24 -r da6d7bc0a8b0 getfastaBed.xml
--- a/getfastaBed.xml	Sun Jan 21 07:16:59 2018 -0500
+++ b/getfastaBed.xml	Fri Feb 09 08:59:46 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_getfastabed" name="GetFastaBed" version="@WRAPPER_VERSION@.1">
     <description>use intervals to extract sequences from a FASTA file</description>
     <macros>
         <import>macros.xml</import>
@@ -34,7 +34,7 @@
             </when>
             <when value="preloaded">
                <param name="fasta_id" type="select">
-                  <options from_data_table="all_fasta" />
+                  <options from_data_table="fasta_indexes" />
                </param>
             </when>
         </conditional>
diff -r 3f852f713d24 -r da6d7bc0a8b0 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Fri Feb 09 08:59:46 2018 -0500
@@ -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    /depot/data2/galaxy/hg19/sam/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    /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full       hg18    Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full       hg19    Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 3f852f713d24 -r da6d7bc0a8b0 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sun Jan 21 07:16:59 2018 -0500
+++ b/tool_data_table_conf.xml.sample	Fri Feb 09 08:59:46 2018 -0500
@@ -4,6 +4,11 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/all_fasta.loc" />
     </table>
+    <!-- Locations of all sam indexes under genome directory -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
     <!-- Locations of all gff files with annotations of genome builds -->
     <table name="all_gff" comment_char="#">
         <columns>value, dbkey, name, path</columns>