# HG changeset patch
# User jackcurragh
# Date 1679909934 0
# Node ID a1565147cdc8eb0d93561cedd3dd3a770cc3372d
# Parent  e8551e16829c828cc9736e1b2b478b1c18c5bcda
Uploaded

diff -r e8551e16829c -r a1565147cdc8 bowtie_genome_wrapper/bowtie_genomic_wrapper.xml
--- a/bowtie_genome_wrapper/bowtie_genomic_wrapper.xml	Sat Aug 20 11:38:29 2022 +0000
+++ b/bowtie_genome_wrapper/bowtie_genomic_wrapper.xml	Mon Mar 27 09:38:54 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="bowtie_genomic_wrapper" name="Bowtie Genome Alignment" version="1.6.0">
+<tool id="bowtie_genomic_wrapper" name="Bowtie Genome Alignment" version="1.7.1">
   <description>Align to the Genome with 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 genome" help="if your genome of interest is not listed - contact Galaxy team">
-          <options from_data_table="bowtie_indexes">
+          <options from_data_table="bowtie_genome_refs2">
             <filter type="sort_by" column="2" />
             <validator type="no_options" message="No indexes are available" />
           </options>
@@ -424,7 +424,7 @@
     <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
   </inputs>
   <outputs>
-    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
+    <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
       <actions>
         <conditional name="refGenomeSource.genomeSource">
           <when value="indexed">
diff -r e8551e16829c -r a1565147cdc8 bowtie_genome_wrapper/tool-data/bowtie_indexes.loc.sample
--- a/bowtie_genome_wrapper/tool-data/bowtie_indexes.loc.sample	Sat Aug 20 11:38:29 2022 +0000
+++ b/bowtie_genome_wrapper/tool-data/bowtie_indexes.loc.sample	Mon Mar 27 09:38:54 2023 +0000
@@ -1,9 +1,24 @@
 mus_musculus_m28	m28	Mus musculus (m28) Genome	/mnt/data/indices/bowtie/genome/mus_musculus_m28/mus_musculus_m28_genome
+mus_musculus_m10	m10	Mus musculus (m10) Genome	/mnt/data/indices/bowtie/genome/mus_musculus_m10/mus_musculus_m10_genome
 drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Genome	/mnt/data/indices/bowtie/genome/drosophila_melanogater_dm6/drosophila_melanogater_dm6_genome
-drosophila_melanogater_dm3  dm3 Drosophila melanogaster (dm3) Genome    /mnt/data/indices/bowtie/genome/drosophila_melanogaster_dm3/drosophila_melanogaster_dm3_genome
+drosophila_melanogater_dm3	dm3	Drosophila melanogaster (dm3) Genome	/mnt/data/indices/bowtie/genome/drosophila_melanogaster_dm3/drosophila_melanogaster_dm3_genome
 sacCer_9	sacCer9	Saccharomyces cerevisiae (v9) Genome	/mnt/data/indices/bowtie/genome/sacCer_9/sacCer_9_genome
-sarCer_3	sacCer3	Saccharomyces cerevisiae (v3) Genome	/mnt/data/indices/bowtie/genome/sacCer_3/sacCer_3_genome
-E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655) Genome	/mnt/data/indices/bowtie/genome/E_coli_K12_MG1655/E_coli_K12_MG1655_genome
+sarCer_3	sacCer3	Saccharomyces cerevisiae (v3) Genome	/mnt/data/indices/bowtie/genome/sacCer_3_gwips/sacCer3_genome
+E_coli_K12_ASM584v2	e_coli_ASM584v2	Escherichia coli (K12 ASM584v2) Genome	/mnt/data/indices/bowtie/genome/E_coli_gwips/ecoli_gwips_genom
 Arabidopsis	araThal	Arabidopsis thaliana (TAIR10) Genome	/mnt/data/indices/bowtie/genome/Arabidopsis/Arabidopsis_genome
 homo_sapiens_hg19	hg19	Homo sapiens (hg19) Genome	/mnt/data/indices/bowtie/genome/homo_sapiens_hg19/homo_sapiens_hg19_genome
-homo_sapiens_hg38	hg38	Homo sapiens (hg38) Genome	/mnt/data/indices/bowtie/genome/homo_sapiens_hg38/homo_sapiens_hg38_genome
\ No newline at end of file
+homo_sapiens_hg38	hg38	Homo sapiens (hg38) Genome	/mnt/data/indices/bowtie/genome/homo_sapiens_hg38/homo_sapiens_hg38_genome
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diff -r e8551e16829c -r a1565147cdc8 bowtie_genome_wrapper/tool_data_table_conf.xml.sample
--- a/bowtie_genome_wrapper/tool_data_table_conf.xml.sample	Sat Aug 20 11:38:29 2022 +0000
+++ b/bowtie_genome_wrapper/tool_data_table_conf.xml.sample	Mon Mar 27 09:38:54 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_indexes" comment_char="#">
+    <table name="bowtie_genome_refs3" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bowtie_indexes.loc" />
     </table>