# HG changeset patch
# User jackcurragh
# Date 1653646325 0
# Node ID 15e6eb67d7100dd6a47b1fae092e1d461cb60d12
# Parent  f6ef1c85b0454090e25be3532be85b03b5b85e84
Uploaded

diff -r f6ef1c85b045 -r 15e6eb67d710 bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml
--- a/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Fri May 13 09:53:29 2022 +0000
+++ b/bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml	Fri May 27 10:12:05 2022 +0000
@@ -1,7 +1,9 @@
-<tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.3.0">
-  <description></description>
+<tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.4.0">
+  <description>Align to Transcriptome using Bowtie</description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
+    <requirement type="package" version="1.13">samtools</requirement>
+
   </requirements>
   <version_command>bowtie --version</version_command>
   <command>
diff -r f6ef1c85b045 -r 15e6eb67d710 bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample
--- a/bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample	Fri May 13 09:53:29 2022 +0000
+++ b/bowtie_transcriptome_wrapper/tool-data/bowtie_transcriptome_indexes.loc.sample	Fri May 27 10:12:05 2022 +0000
@@ -1,10 +1,10 @@
-homo_sapiens_gencode39	hg_gen39	Homo sapiens (gencode 39) Transcriptome	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode39/homo_sapiens_gencode39_transcriptome
-homo_sapiens_gencode28	hg_gen28	Homo sapiens (gencode 28) Transcriptome	/data2/indices/bowtie/transcriptome/homo_sapiens_gencode28/homo_sapiens_gencode28_transcriptome
-mus_musculus_m28	m28	Mus musculus (m28) Transcriptome	/data2/indices/bowtie/transcriptome/mus_musculus_m28/mus_musculus_m28_transcriptome
-mus_musculus_m10	m10	Mus musculus (m10) Transcriptome	/data2/indices/bowtie/transcriptome/mus_musculus_m10/mus_musculus_m10_transcriptome
-drosophila_melanogaster_dm3	dm3	Drosophila melanogaster (dm3) Transcriptome	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm3/drosophila_melanogater_dm3_transcriptome
-drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Transcriptome	/data2/indices/bowtie/transcriptome/drosophila_melanogater_dm6/drosophila_melanogater_dm6_transcriptome
-sacCer_9	sacCer9	Saccharomyces cerevisiae (v9) Transcriptome	/data2/indices/bowtie/transcriptome/sacCer_9/sacCer_9_transcriptome
-sarCer_3	sacCer3	Saccharomyces cerevisiae (v3) Transcriptome	/data2/indices/bowtie/transcriptome/sacCer_3/sacCer_3_transcriptome
-E_coli_K12_MG1655	e_coli	Escherichia coli (K12 MG1655) Transcriptome	/data2/indices/bowtie/transcriptome/E_coli_K12_MG1655/E_coli_K12_MG1655_transcriptome
-Arabidopsis	araThal	Arabidopsis thaliana (TAIR10) Transcriptome	/data2/indices/bowtie/transcriptome/Arabidopsis/Arabidopsis_transcriptome
+homo_sapiens_gencode39	hg_gen39	Homo sapiens (gencode 39) Transcriptome	/mnt/data/indices/bowtie/transcriptome/homo_sapiens_gencode39/homo_sapiens_gencode39_transcriptome
+homo_sapiens_gencode28	hg_gen28	Homo sapiens (gencode 28) Transcriptome	/mnt/data/indices/bowtie/transcriptome/homo_sapiens_gencode28/homo_sapiens_gencode28_transcriptome
+mus_musculus_m28	m28	Mus musculus (m28) Transcriptome	/mnt/data/indices/bowtie/transcriptome/mus_musculus_m28/mus_musculus_m28_transcriptome
+mus_musculus_m10	m10	Mus musculus (m10) Transcriptome	/mnt/data/indices/bowtie/transcriptome/mus_musculus_m10/mus_musculus_m10_transcriptome
+drosophila_melanogaster_dm3	dm3	Drosophila melanogaster (dm3) Transcriptome	/mnt/data/indices/bowtie/transcriptome/drosophila_melanogater_dm3/drosophila_melanogater_dm3_transcriptome
+drosophila_melanogaster_dm6	dm6	Drosophila melanogaster (dm6) Transcriptome	/mnt/data/indices/bowtie/transcriptome/drosophila_melanogater_dm6/drosophila_melanogater_dm6_transcriptome
+sacCer_9	sacCer9	Saccharomyces cerevisiae (v9) Transcriptome	/mnt/data/indices/bowtie/transcriptome/sacCer_9/sacCer_9_transcriptome
+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