Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

changeset 19:d8cc5dbc9fa8 draft

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Uploaded
author triasteran
date Mon, 13 Feb 2023 11:56:57 +0000
parents 6562f4079f46
children 5948fc162f8c
files trips_bam_to_sqlite/tool-data/builtin_sqlites.loc.sample trips_bam_to_sqlite/tool_data_table_conf.xml.sample trips_bam_to_sqlite/trips_bam_to_sqlite.xml
diffstat 3 files changed, 4 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/trips_bam_to_sqlite/tool-data/builtin_sqlites.loc.sample	Mon Feb 13 11:28:43 2023 +0000
+++ b/trips_bam_to_sqlite/tool-data/builtin_sqlites.loc.sample	Mon Feb 13 11:56:57 2023 +0000
@@ -6,6 +6,4 @@
 mus_musculus_m14	m14	Mus musculus (Gencode m14)	/mnt/data/organism_sqlites/mus_musculus_m14/mus_musculus.gencode14.sqlite
 mus_musculus_m28	m28	Mus musculus (Gencode m28)	/mnt/data/organism_sqlites/mus_musculus_m28/mus_musculus.gencode28.sqlite
 Escherichia_coli_str_k_12_ASM584v2	Ecoli_ASM584v2	Escherichia coli str k12 ASM584v2	/mnt/data/organism_sqlites/E_coli_trips/escherichia_coli.Ensembl_k_12_ASM584v2.sqlite
-sacCer_sgd_R64-1-1	sacCer3_sgd_R64-1-1	Saccharomyces cerevisiae (sgd sacCer3 R64-1-1)	/mnt/data/organism_sqlites/sacCer_R64/Saccharomyces_cerevisiae.R64.sqlite
-
-
+Saccharomyces_cerevisiae_sgd_R64-1-1	sacCer3_sgd_R64-1-1	Saccharomyces cerevisiae (sgd sacCer3 R64-1-1)	/mnt/data/organism_sqlites/sacCer_3_sgd_R64/saccer3_trips_working.sqlite
--- a/trips_bam_to_sqlite/tool_data_table_conf.xml.sample	Mon Feb 13 11:28:43 2023 +0000
+++ b/trips_bam_to_sqlite/tool_data_table_conf.xml.sample	Mon Feb 13 11:56:57 2023 +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 sqlites in the Trips-Viz format-->
-    <table name="sqlites_upd" comment_char="#">
+    <table name="sqlites_upd1" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/builtin_sqlites.loc" />
     </table>
--- a/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Mon Feb 13 11:28:43 2023 +0000
+++ b/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Mon Feb 13 11:56:57 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.8">
+<tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.8a">
     <description>Convert BAM file to SQLITE for Trips-Viz</description>
     <requirements>
         <requirement type="package" version="0.19.0">pysam</requirement>
@@ -24,7 +24,7 @@
             </param>
             <when value="builtin">
                 <param name="input2_builtin" type="select" format="sqlite" label="Select a SQLITE" help="if your organism of interest is not listed - contact RiboGalaxy team">
-                    <options from_data_table="sqlites_upd">
+                    <options from_data_table="sqlites_upd1">
                         <filter type="sort_by" column="2" />
                         <validator type="no_options" message="No built-ins are available" />
                     </options>