# HG changeset patch
# User triasteran
# Date 1648398168 0
# Node ID cd79614871c2106aaa629eeb4ee5575b9e0ba7dd
# Parent  14fb4b4872e398e0866a417faeba22d936c09f42
index table name has changed
absolute path to indexes are added

diff -r 14fb4b4872e3 -r cd79614871c2 bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml
--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Tue Mar 22 12:34:36 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Sun Mar 27 16:22:48 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.2.0">
+<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.3.0ind">
   <description></description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -160,7 +160,7 @@
       </param>
       <when value="indexed">
         <param name="index" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
-          <options from_data_table="bowtie_indexes">
+          <options from_data_table="bowtie_indexes_transcriptome">
             <filter type="sort_by" column="2" />
             <validator type="no_options" message="No indexes are available" />
           </options>
diff -r 14fb4b4872e3 -r cd79614871c2 bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample
--- a/bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample	Tue Mar 22 12:34:36 2022 +0000
+++ b/bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample	Sun Mar 27 16:22:48 2022 +0000
@@ -1,37 +1,5 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Bowtie indexed sequences data files. You will
-#need to create these data files and then create a bowtie_indices.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The bowtie_indices.loc
-#file has this format (longer white space characters are TAB characters):
-#
 #<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
-#
-#So, for example, if you had hg18 indexed stored in
-#/depot/data2/galaxy/bowtie/hg18/,
-#then the bowtie_indices.loc entry would look like this:
-#
-#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
-#
-#and your /depot/data2/galaxy/bowtie/hg18/ directory
-#would contain hg18.*.ebwt files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
-#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
-#...etc...
-#
-#Your bowtie_indices.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:
-#
-#hg18canon			hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
-#hg18full			hg18	hg18 Full		/depot/data2/galaxy/bowtie/hg18/hg18full
-#/orig/path/hg19	hg19	hg19			/depot/data2/galaxy/bowtie/hg19/hg19
-#...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.
-#
+hg38_gencode25_transcriptome	hg38_gencode25_transcriptome	hg38_gencode25_transcriptome	/data/transcriptome/homo_sapiens_gencode25/gencode_v25_human
+mus_musculus_transcriptome	mus_musculus_transcriptome	mus_musculus_transcriptome	/data/transcriptome/Mus_musculus/mus_musculus
+ecoli_transcriptome	ecoli_transcriptome	ecoli_transcriptome	/data/transcriptome/e_coli/ecoli 
+sacCer3_transcriptome	sacCer3_transcriptome	sacCer3_transcriptome	/data/transcriptome/saccharomyces_cerevisiae/yeast_index
diff -r 14fb4b4872e3 -r cd79614871c2 bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample
--- a/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Tue Mar 22 12:34:36 2022 +0000
+++ b/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Sun Mar 27 16:22:48 2022 +0000
@@ -1,7 +1,7 @@
 <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
 <tables>
     <!-- Locations of indexes in the Bowtie mapper format -->
-    <table name="bowtie_indexes" comment_char="#">
+    <table name="bowtie_indexes_transcriptome" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bowtie_indices.loc" />
     </table>