Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome

changeset 3:14deb381fa27 draft

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Uploaded
author jackcurragh
date Tue, 05 Apr 2022 12:53:59 +0000
parents cd79614871c2
children 5c1eed27d85a
files bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample
diffstat 3 files changed, 13 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Sun Mar 27 16:22:48 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Tue Apr 05 12:53:59 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.3.0ind">
+<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.2.0">
   <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_transcriptome">
+          <options from_data_table="bowtie_indexes">
             <filter type="sort_by" column="2" />
             <validator type="no_options" message="No indexes are available" />
           </options>
--- a/bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample	Sun Mar 27 16:22:48 2022 +0000
+++ b/bowtie_transcriptome_wrapper/tool-data/bowtie_indices.loc.sample	Tue Apr 05 12:53:59 2022 +0000
@@ -1,5 +1,10 @@
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
-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
+homo_sapiens_gencode39	hg_gen39	Homo sapiens (genocode 39)	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode39_transcriptome
+homo_sapiens_gencode28	hg_gen28	Homo sapiens (genocode 28)	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode39_transcriptome
+mus_musculus_m28	m28	Mus musculus (m28)	/data2/indices/bowtie/transcriptome/mus_musculus_m28/mus_musculus_m28_transcriptome
+mus_musculus_m10	m10	Mus musculus (m10)	/data2/indices/bowtie/transcriptome/mus_musculus_m10/mus_musculus_m10_transcriptome
+drosophila_melanogaster_dm3	dm3	Drosophila melanogaster (dm3)	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm3_transcriptome
+drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6)	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm6_transcriptome
+sacCer_9	sacCer9	Saccharomyces cerevisiae (v9)	/data2/indices/bowtie/transcriptome/sacCer_9/sacCer_9_transcriptome
+sarCer_3	sacCer3	Saccharomyces cerevisiae (v3)	/data2/indices/bowtie/transcriptome/sacCer_3/sacCer_3_transcriptome
+E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655)	/data2/indices/bowtie/transcriptome/E_coli_K12_MG1655_transcriptome
+Arabidopsis	araThal	Arabidopsis thaliana (TAIR10)	/data2/indices/bowtie/transcriptome/Arabidopsis/Arabidopsis_transcriptome
--- a/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Sun Mar 27 16:22:48 2022 +0000
+++ b/bowtie_transcriptome_wrapper/tool_data_table_conf.xml.sample	Tue Apr 05 12:53:59 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_transcriptome" comment_char="#">
+    <table name="bowtie_indexes" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bowtie_indices.loc" />
     </table>