# HG changeset patch
# User thondeboer
# Date 1526504571 14400
# Node ID 7d10b55965c9589ce50c72b08781e93b6d6ecfd9
# Parent  441103f02a1199636d8e0dcbabe1c0c453062299
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

diff -r 441103f02a11 -r 7d10b55965c9 computeGC.xml
--- a/computeGC.xml	Wed May 16 02:05:26 2018 -0400
+++ b/computeGC.xml	Wed May 16 17:02:51 2018 -0400
@@ -45,7 +45,7 @@
 			   type="select"
 			   label="Select a built-in reference sequence"
 			   help="The reference sequence that will be used as the basis for the simulated reads">
-		  <options from_data_table="all_fasta" />
+		  <options from_data_table="fasta_indexes" />
 		</param>
 	  </when>
 	  <when value="history">
diff -r 441103f02a11 -r 7d10b55965c9 genMutModel.xml
--- a/genMutModel.xml	Wed May 16 02:05:26 2018 -0400
+++ b/genMutModel.xml	Wed May 16 17:02:51 2018 -0400
@@ -50,7 +50,7 @@
 			   type="select"
 			   label="Select a built-in reference sequence"
 			   help="The reference sequence that will be used as the basis for the simulated reads">
-		  <options from_data_table="all_fasta" />
+		  <options from_data_table="fasta_indexes" />
 		</param>
 	  </when>
 	  <when value="history">
@@ -180,5 +180,16 @@
 			<output name="trinuc_file" value="chrMT.fa.trinucCounts" compare="diff"/>
 		</test>
 
+		<test>
+			<conditional name="in_type">
+				<param name="input_type" value="built-in"/>
+			  <param name="reference" value="hg19chrmt" format="fasta">
+			     <options from_data_table="fasta_indexes" />
+			  </param>
+			</conditional>
+			<param name="mutation_file" value="chrMT-PE-VCF-BAM.vcf"/>
+			<output name="genMutModel_modelfile" value="chrMT-PE-VCF-BAM-genMutModel.p" compare="diff"/>
+		</test>
+		
 	</tests>
 </tool>
\ No newline at end of file
diff -r 441103f02a11 -r 7d10b55965c9 neat_genreads.xml
--- a/neat_genreads.xml	Wed May 16 02:05:26 2018 -0400
+++ b/neat_genreads.xml	Wed May 16 17:02:51 2018 -0400
@@ -97,7 +97,7 @@
 			   type="select"
 			   label="Select a built-in reference sequence"
 			   help="The reference sequence that will be used as the basis for the simulated reads">
-		  <options from_data_table="all_fasta" />
+		  <options from_data_table="fasta_indexes" />
 		</param>
 	  </when>
 	  <when value="history">
@@ -627,6 +627,28 @@
 			<assert_stdout has_text="Writing output VCF..."/>
 		</test>
 
-
+		<test>
+			<conditional name="in_type">
+				<param name="input_type" value="built-in"/>
+			  <param name="reference" value="hg19chrmt" format="fasta">
+			     <options from_data_table="fasta_indexes" />
+			  </param>
+			</conditional>
+			<conditional name="lib_type_cond">
+				<param name="lib_type" value="single"/>
+			</conditional>
+			<section name="stats">
+				<param name="seed" value="1"/>
+			</section>
+			<param name="read_length" value="101"/>
+			<section name="out_options">
+				<param name="prefix" value="out"/>
+				<param name="golden_bam" value="false"/>
+				<param name="golden_vcf" value="false"/>
+				<param name="compress" value="false"/>
+			</section>
+			<output name="out_file1" file="chrMT_read1.fq" compare="diff"/>
+		</test>
+		
 	</tests>
 </tool>
\ No newline at end of file
diff -r 441103f02a11 -r 7d10b55965c9 test-data/fasta_indexes.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc	Wed May 16 17:02:51 2018 -0400
@@ -0,0 +1,30 @@
+#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
+hg19chrmt	hg19	Human (Homo sapiens): hg19 chrMT	${__HERE__}/chrMT.fa
\ No newline at end of file
diff -r 441103f02a11 -r 7d10b55965c9 tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Wed May 16 02:05:26 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +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.
-#
diff -r 441103f02a11 -r 7d10b55965c9 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Wed May 16 17:02:51 2018 -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    /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
\ No newline at end of file
diff -r 441103f02a11 -r 7d10b55965c9 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed May 16 02:05:26 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Wed May 16 17:02:51 2018 -0400
@@ -1,7 +1,7 @@
 <tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+    <!-- Locations of all sam indexes under genome directory -->
+    <table name="fasta_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
+        <file path="tool-data/fasta_indexes.loc" />
     </table>
 </tables>
diff -r 441103f02a11 -r 7d10b55965c9 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed May 16 17:02:51 2018 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all sam indexes under genome directory -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+</tables>
\ No newline at end of file