# HG changeset patch
# User elixir-it
# Date 1569086548 14400
# Node ID f7d69881bdec5a1df92dd04a65293146291bcf2c
# Parent  2ff18e84c946648a41ab7ad7e45107e23cf45b8a
Uploaded

diff -r 2ff18e84c946 -r f7d69881bdec somatic_sniper.xml
--- a/somatic_sniper.xml	Mon Jul 02 11:37:26 2018 -0400
+++ b/somatic_sniper.xml	Sat Sep 21 13:22:28 2019 -0400
@@ -19,7 +19,7 @@
 
 	
   ## BUILD SOMATICSNIPER COMMAND LINE 
-  \$CONDA_DEFAULT_ENV/bin/bam-somaticsniper
+  bam-somaticsniper
     -F vcf
     -q $advancedsettings.q
     -Q $advancedsettings.Q
@@ -83,7 +83,7 @@
 			</param>
 			<when value="cached">
 				<param name="index" type="select" label="Reference Genome File" >
-					<options from_data_table="all_fasta" />
+					<options from_data_table="sniper_index" />
 				</param>
       			</when>
       			<when value="history">
@@ -118,5 +118,8 @@
         </tests>
 	<help>
 		http://gmt.genome.wustl.edu/packages/somatic-sniper/
+
+this wrapper was developed from https://github.com/morinlab/tools-morinlab/tree/master/tools/somatic_sniper only the requirement and part of the command line have been changed in order to make it suitable for CONDA
+
 	</help>
 </tool>
diff -r 2ff18e84c946 -r f7d69881bdec tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Mon Jul 02 11:37:26 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 2ff18e84c946 -r f7d69881bdec tool-data/sniper_index.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sniper_index.loc.sample	Sat Sep 21 13:22:28 2019 -0400
@@ -0,0 +1,34 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of somatic-sniper indexed sequences data files. You will need
+#to create these data files and then create a sniper_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The sniper_index.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_path>
+#
+#So, for example, if you had phiX indexed stored in 
+#/depot/data2/galaxy/phiX/base/, 
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174   phiX   phiX Pretty   /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.dict, phiX.fa.fai files.
+#
+#
+#Your sniper_index.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files.  For example:
+#
+#phiX174                                phiX    phiX174                 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon                              hg18    hg18 Canonical  /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full                               hg18    hg18 Full               /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa             hg19    hg19                    /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#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. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 2ff18e84c946 -r f7d69881bdec tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Jul 02 11:37:26 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Sat Sep 21 13:22:28 2019 -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  sniper index under genome directory  -->
+    <table name="sniper_index" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/all_fasta.loc" />
+        <file path="tool-data/sniper_index.loc" />
     </table>
 </tables>