Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome

changeset 16:bff7f8f0ba98 draft

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author jackcurragh
date Thu, 09 Feb 2023 14:25:30 +0000
parents 9bef8486912e
children 816d9c5ef4a8
files bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample
diffstat 3 files changed, 5 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Thu Feb 09 13:30:35 2023 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Thu Feb 09 14:25:30 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.7.1">
+<tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.7.2">
   <description>Align to Transcriptome using Bowtie</description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
@@ -162,7 +162,7 @@
       </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_transcriptome_indexes_2">
+          <options from_data_table="bowtie_transcriptome_indexes">
             <filter type="sort_by" column="2" />
             <validator type="no_options" message="No indexes are available" />
           </options>
--- a/bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample	Thu Feb 09 13:30:35 2023 +0000
+++ b/bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample	Thu Feb 09 14:25:30 2023 +0000
@@ -11,3 +11,5 @@
 sarCer_3	sacCer3	Saccharomyces cerevisiae (v3) Transcriptome	/mnt/data/indices/bowtie/transcriptome/sacCer_3/sacCer_3_transcriptome
 E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655) Transcriptome	/mnt/data/indices/bowtie/transcriptome/E_coli_K12_MG1655/E_coli_K12_MG1655_transcriptome
 Arabidopsis	araThal	Arabidopsis thaliana (TAIR10) Transcriptome	/mnt/data/indices/bowtie/transcriptome/Arabidopsis/Arabidopsis_transcriptome
+mus_musculus_m25	m25	Mus musculus test Transcriptome	/mnt/data/indices/bowtie/transcriptome/mus_musculus_m25/mus_musculus_m25_transcriptome
+
--- a/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Thu Feb 09 13:30:35 2023 +0000
+++ b/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Thu Feb 09 14:25:30 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 indexes in the Bowtie mapper format -->
-    <table name="bowtie_transcriptome_indexes_2" comment_char="#">
+    <table name="bowtie_transcriptome_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bowtie_transcriptome_indexes.loc" />
     </table>