Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna

changeset 25:6e58b540807d draft

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author jackcurragh
date Fri, 27 May 2022 10:04:45 +0000
parents ef1a6b28b664
children 7065bba6e7cd
files bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml bowtie_rRNA_removal_wrapper/tool-data/bowtie_rRNA_indexes.loc.sample
diffstat 2 files changed, 16 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml	Thu May 12 14:19:59 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_tRNA_removal_wrapper.xml	Fri May 27 10:04:45 2022 +0000
@@ -1,7 +1,9 @@
-<tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Remove rRNA and tRNA using Bowtie" version="1.6.0">
-  <description></description>
+<tool id="bowtie_rRNA_tRNA_removal_wrapper" name="Bowtie ncRNA removal" version="1.7.0">
+  <description>Remove rRNA and tRNA 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>
--- a/bowtie_rRNA_removal_wrapper/tool-data/bowtie_rRNA_indexes.loc.sample	Thu May 12 14:19:59 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/tool-data/bowtie_rRNA_indexes.loc.sample	Fri May 27 10:04:45 2022 +0000
@@ -1,12 +1,12 @@
-sacCer9rRNA	sacCer9	Saccharomyces cerevisiae rRNA	/data2/indices/bowtie/ncRNA/sacCer_9/sacCer_9_rRNA
-sacCer9tRNA	sacCer9	Saccharomyces cerevisiae tRNA	/data2/indices/bowtie/ncRNA/sacCer_9/sacCer_9_tRNA
-hg38rRNA	hg38	Homo sapiens rRNA	/data2/indices/bowtie/ncRNA/homo_sapiens_hg38/homo_sapiens_hg38_rRNA
-hg38tRNA	hg38	Homo sapiens tRNA	/data2/indices/bowtie/ncRNA/homo_sapiens_hg38/homo_sapiens_hg38_tRNA
-e_colirRNA	e_coli	Escherichia coli rRNA	/data2/indices/bowtie/ncRNA/E_coli_K12_MG1655/E_coli_K12_MG1655_rRNA
-e_colitRNA	e_coli	Escherichia coli tRNA	/data2/indices/bowtie/ncRNA/E_coli_K12_MG1655/E_coli_K12_MG1655_tRNA
-dm6rRNA	dm6	Drosophila melanogater rRNA	/data2/indices/bowtie/ncRNA/drosophila_melanogater_dm6/drosophila_melanogater_dm6_rRNA
-dm6tRNA	dm6	Drosophila melanogater tRNA	/data2/indices/bowtie/ncRNA/drosophila_melanogater_dm6/drosophila_melanogater_dm6_tRNA
-m28rRNA	m28	Mus musculus rRNA	/data2/indices/bowtie/ncRNA/mus_musculus_m28/mus_musculus_m28_rRNA
-m28tRNA	m28	Mus musculus tRNA	/data2/indices/bowtie/ncRNA/mus_musculus_m28/mus_musculus_m28_tRNA
-araThalrRNA	araThal	Arabidopsis thaliana (TAIR10) rRNA	/data2/indices/bowtie/ncRNA/Arabidopsis/Arabidopsis_rRNA
-araThaltRNA	araThal	Arabidopsis thaliana (TAIR10) tRNA	/data2/indices/bowtie/ncRNA/Arabidopsis/Arabidopsis_tRNA
\ No newline at end of file
+sacCer9rRNA	sacCer9	Saccharomyces cerevisiae rRNA	/mnt/data/indices/bowtie/ncRNA/sacCer_9/sacCer_9_rRNA
+sacCer9tRNA	sacCer9	Saccharomyces cerevisiae tRNA	/mnt/data/indices/bowtie/ncRNA/sacCer_9/sacCer_9_tRNA
+hg38rRNA	hg38	Homo sapiens rRNA	/mnt/data/indices/bowtie/ncRNA/homo_sapiens_hg38/homo_sapiens_hg38_rRNA
+hg38tRNA	hg38	Homo sapiens tRNA	/mnt/data/indices/bowtie/ncRNA/homo_sapiens_hg38/homo_sapiens_hg38_tRNA
+e_colirRNA	e_coli	Escherichia coli rRNA	/mnt/data/indices/bowtie/ncRNA/E_coli_K12_MG1655/E_coli_K12_MG1655_rRNA
+e_colitRNA	e_coli	Escherichia coli tRNA	/mnt/data/indices/bowtie/ncRNA/E_coli_K12_MG1655/E_coli_K12_MG1655_tRNA
+dm6rRNA	dm6	Drosophila melanogater rRNA	/mnt/data/indices/bowtie/ncRNA/drosophila_melanogater_dm6/drosophila_melanogater_dm6_rRNA
+dm6tRNA	dm6	Drosophila melanogater tRNA	/mnt/data/indices/bowtie/ncRNA/drosophila_melanogater_dm6/drosophila_melanogater_dm6_tRNA
+m28rRNA	m28	Mus musculus rRNA	/mnt/data/indices/bowtie/ncRNA/mus_musculus_m28/mus_musculus_m28_rRNA
+m28tRNA	m28	Mus musculus tRNA	/mnt/data/indices/bowtie/ncRNA/mus_musculus_m28/mus_musculus_m28_tRNA
+araThalrRNA	araThal	Arabidopsis thaliana (TAIR10) rRNA	/mnt/data/indices/bowtie/ncRNA/Arabidopsis/Arabidopsis_rRNA
+araThaltRNA	araThal	Arabidopsis thaliana (TAIR10) tRNA	/mnt/data/indices/bowtie/ncRNA/Arabidopsis/Arabidopsis_tRNA
\ No newline at end of file