Mercurial > repos > jackcurragh > ribogalaxy_bowtie_rrna

changeset 9:82854aad329b draft

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Uploaded
author triasteran
date Wed, 23 Mar 2022 17:48:46 +0000
parents 8ae1d397d66d
children 2debb30fefd4
files bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml bowtie_rRNA_removal_wrapper/tool-data/bowtie_indices.loc bowtie_rRNA_removal_wrapper/tool-data/bowtie_indices.loc.sample bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml.sample
diffstat 6 files changed, 12 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py	Wed Mar 23 11:30:44 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.py	Wed Mar 23 17:48:46 2022 +0000
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """
 Runs Bowtie on single-end or paired-end data.
--- a/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml	Wed Mar 23 11:30:44 2022 +0000
+++ b/bowtie_rRNA_removal_wrapper/bowtie_rRNA_removal_wrapper.xml	Wed Mar 23 17:48:46 2022 +0000
@@ -1,11 +1,11 @@
-<tool id="bowtie_rRNA_removal_wrapper" name="Remove rRNA using Bowtie" version="1.4.0b">
+<tool id="bowtie_rRNA_removal_wrapper" name="Remove rRNA using Bowtie" version="1.4.0c">
   <description></description>
   <requirements>
     <requirement type="package" version="1.2.0">bowtie</requirement>
   </requirements>
   <version_command>bowtie --version</version_command>
   <command>
-    python '$__tool_directory__/bowtie_rRNA_removal_wrapper.py'
+    python3 '$__tool_directory__/bowtie_rRNA_removal_wrapper.py'
       ## Set number of threads
       --threads="\${GALAXY_SLOTS:-4}"
       ## Outputs
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_rRNA_removal_wrapper/tool-data/bowtie_indices.loc	Wed Mar 23 17:48:46 2022 +0000
@@ -0,0 +1,1 @@
+sacCer3_rRNA	sacCer3_rRNA 	sacCer3_rRNA 	/home/alla/indices/sacCer3_rRNA_bowtie/yeast_rRNA
\ No newline at end of file
--- a/bowtie_rRNA_removal_wrapper/tool-data/bowtie_indices.loc.sample	Wed Mar 23 11:30:44 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-sacCer3_rRNA  sacCer3_rRNA  sacCer3_rRNA  /home/alla/indices/sacCer3_rRNA_bowtie/yeast_rRNA
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml	Wed Mar 23 17:48:46 2022 +0000
@@ -0,0 +1,8 @@
+<!-- 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="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/bowtie_indices.loc" />
+    </table>
+</tables>
--- a/bowtie_rRNA_removal_wrapper/tool_data_table_conf.xml.sample	Wed Mar 23 11:30:44 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<!-- 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="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices.loc" />
-    </table>
-</tables>