# HG changeset patch
# User artbio
# Date 1504086018 14400
# Node ID 320e06bf99b9d6601bd6906c310d521dd50e754d
# Parent  6f1378738798a577e5e007b21a74891b7196c3ff
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 5cf421cdafd250995172684a9db0ac8acbb350b5

diff -r 6f1378738798 -r 320e06bf99b9 overlapping_reads.xml
--- a/overlapping_reads.xml	Tue Aug 29 20:02:15 2017 -0400
+++ b/overlapping_reads.xml	Wed Aug 30 05:40:18 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.0">
+<tool id="overlapping_reads" name="Get overlapping reads" version="0.9.1">
     <description />
     <requirements>
         <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
diff -r 6f1378738798 -r 320e06bf99b9 tool-data/bowtie_indices.loc.sample
--- a/tool-data/bowtie_indices.loc.sample	Tue Aug 29 20:02:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Bowtie indexed sequences data files. You will
-#need to create these data files and then create a bowtie_indices.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The bowtie_indices.loc
-#file has this format (longer white space characters are TAB characters):
-#
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
-#
-#So, for example, if you had hg18 indexed stored in
-#/depot/data2/galaxy/bowtie/hg18/,
-#then the bowtie_indices.loc entry would look like this:
-#
-#hg18	hg18	hg18	/depot/data2/galaxy/bowtie/hg18/hg18
-#
-#and your /depot/data2/galaxy/bowtie/hg18/ directory
-#would contain hg18.*.ebwt files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
-#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
-#...etc...
-#
-#Your bowtie_indices.loc file should include an entry per line for each
-#index set you have stored. The "file" in the path does not actually
-#exist, but it is the prefix for the actual index files. For example:
-#
-#hg18canon	 hg18	hg18 Canonical	/depot/data2/galaxy/bowtie/hg18/hg18canon
-#hg18full	 hg18	hg18 Full	 /depot/data2/galaxy/bowtie/hg18/hg18full
-#/orig/path/hg19	hg19	hg19	 /depot/data2/galaxy/bowtie/hg19/hg19
-#...etc...
-#
-#Note that for backwards compatibility with workflows, the unique ID of
-#an entry must be the path that was in the original loc file, because that
-#is the value stored in the workflow for that parameter. That is why the
-#hg19 entry above looks odd. New genomes can be better-looking.
-#
diff -r 6f1378738798 -r 320e06bf99b9 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Aug 29 20:02:15 2017 -0400
+++ /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>
diff -r 6f1378738798 -r 320e06bf99b9 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Aug 29 20:02:15 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="bowtie" version="1.1.2">
-      <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="pysam" version="0.8.3">
-      <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.9">
-        <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="R" version="3.1.2">
-        <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="biocbasics" version="2.14">
-        <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>