Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

changeset 18:6562f4079f46 draft

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Uploaded
author triasteran
date Mon, 13 Feb 2023 11:28:43 +0000
parents 915a577e6d71
children d8cc5dbc9fa8
files trips_bam_to_sqlite/test-data/test.bam trips_bam_to_sqlite/test-data/test.bamv2.sqlite trips_bam_to_sqlite/test-data/test_n_sorted.bam trips_bam_to_sqlite/test-data/test_n_sorted.bam_n_sorted.bam trips_bam_to_sqlite/test-data/test_n_sorted.bamv2.sqlite trips_bam_to_sqlite/test-data/test_org.sqlite trips_bam_to_sqlite/test-data/test_organism.sqlite trips_bam_to_sqlite/test-data/test_sorted.bam trips_bam_to_sqlite/test-data/test_sorted.bamv2.sqlite 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 11 files changed, 8 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
Binary file trips_bam_to_sqlite/test-data/test.bam has changed
Binary file trips_bam_to_sqlite/test-data/test.bamv2.sqlite has changed
Binary file trips_bam_to_sqlite/test-data/test_n_sorted.bam has changed
Binary file trips_bam_to_sqlite/test-data/test_n_sorted.bam_n_sorted.bam has changed
Binary file trips_bam_to_sqlite/test-data/test_n_sorted.bamv2.sqlite has changed
Binary file trips_bam_to_sqlite/test-data/test_org.sqlite has changed
Binary file trips_bam_to_sqlite/test-data/test_sorted.bam has changed
Binary file trips_bam_to_sqlite/test-data/test_sorted.bamv2.sqlite has changed
--- a/trips_bam_to_sqlite/tool-data/builtin_sqlites.loc.sample	Thu Feb 09 11:42:00 2023 +0000
+++ b/trips_bam_to_sqlite/tool-data/builtin_sqlites.loc.sample	Mon Feb 13 11:28:43 2023 +0000
@@ -1,9 +1,11 @@
 arabidopsis_thaliana_TAIR10	TAIR10	Arabidopsis thaliana (TAIR10)	/mnt/data/organism_sqlites/Arabidopsis/arabidopsis_thaliana.TAIR10.sqlite
-Escherichia_coli_str_k_12_substr_mg1655	Ecoli	Escherichia coli str k12 substr mg1655	/mnt/data/organism_sqlites/E_coli_K12_MG1655/Escherichia_coli_str_k_12_substr_mg1655.sqlite
 homo_sapiens_gencode25	g25	Homo sapiens (Gencode 25)	/mnt/data/organism_sqlites/homo_sapiens_gencode25/homo_sapiens.gencode25.sqlite
 homo_sapiens_gencode28	g28	Homo sapiens (Gencode 28)	/mnt/data/organism_sqlites/homo_sapiens_gencode28/homo_sapiens.gencode28.sqlite
 homo_sapiens_gencode39	g39	Homo sapiens (Gencode 39)	/mnt/data/organism_sqlites/homo_sapiens_gencode39/homo_sapiens.gencode39.sqlite
 mus_musculus_m10	m10	Mus musculus (Gencode m10)	/mnt/data/organism_sqlites/mus_musculus_m10/mus_musculus.gencode10.sqlite
 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
-sacCer_R64	R64	Saccharomyces cerevisiae (R64)	/mnt/data/organism_sqlites/sacCer_R64/Saccharomyces_cerevisiae.R64.sqlite
\ No newline at end of file
+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
+
+
--- a/trips_bam_to_sqlite/tool_data_table_conf.xml.sample	Thu Feb 09 11:42:00 2023 +0000
+++ b/trips_bam_to_sqlite/tool_data_table_conf.xml.sample	Mon Feb 13 11:28:43 2023 +0000
@@ -1,8 +1,8 @@
 <!-- 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" comment_char="#">
+    <table name="sqlites_upd" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/builtin_sqlites.loc" />
     </table>
-</tables>
\ No newline at end of file
+</tables>
--- a/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Thu Feb 09 11:42:00 2023 +0000
+++ b/trips_bam_to_sqlite/trips_bam_to_sqlite.xml	Mon Feb 13 11:28:43 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.7">
+<tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.8">
     <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">
+                    <options from_data_table="sqlites_upd">
                         <filter type="sort_by" column="2" />
                         <validator type="no_options" message="No built-ins are available" />
                     </options>