# HG changeset patch
# User bgruening
# Date 1442522944 14400
# Node ID 07b6202d71e213a6f8f0541a3063d6c69d5bdc9c

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty

diff -r 000000000000 -r 07b6202d71e2 dot2ct.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dot2ct.xml	Thu Sep 17 16:49:04 2015 -0400
@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="rnastructure_dot2ct" name="Dot-Bracket to Connect Table (CT)" version="5.7.a">
+    <description>Converts the first sequence in a Dot-Bracket file into a CT file</description>
+    <requirements>
+        <requirement type="package" version="5.7">rnastructure</requirement>
+    </requirements>
+    
+    <version_command>dot2ct --version | grep -i version</version_command>
+    
+    <command>
+        dot2ct
+            $dotbracket_structure
+            $ct_structure
+    </command>
+    
+    <inputs>
+        <param format="dbn" name="dotbracket_structure" type="data" label="Alignment in BAM or SAM format" />
+    </inputs>
+    
+    <outputs>
+        <data format="txt" name="ct_structure" label="${tool.name} on ${dotbracket_structure.name}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="dotbracket_structure" value="example1_input.dot-bracket.txt" format="dbn" />
+            
+            <output name="ct_structure" file="example1_output_seq1.ct.txt" />     
+        </test>
+    </tests>
+    
+    <help>Convert a Dot-Bracket file into a Connect Table.</help>
+    
+    <citations>
+        <citation type="doi">10.1186/1471-2105-11-129</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 07b6202d71e2 test-data/example1_input.dot-bracket.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example1_input.dot-bracket.txt	Thu Sep 17 16:49:04 2015 -0400
@@ -0,0 +1,9 @@
+>seq1
+GGGCCCaaaGGGCCC
+((((((...))))))
+>seq2
+GGGCCCaaaGGGCCC
+((.(((...))))))
+>seq3
+GGGCCCaaaGGGCCC
+((((((...))).))
diff -r 000000000000 -r 07b6202d71e2 test-data/example1_output_seq1.ct.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example1_output_seq1.ct.txt	Thu Sep 17 16:49:04 2015 -0400
@@ -0,0 +1,16 @@
+   15  seq1
+    1 G       0    2   15    1
+    2 G       1    3   14    2
+    3 G       2    4   13    3
+    4 C       3    5   12    4
+    5 C       4    6   11    5
+    6 C       5    7   10    6
+    7 a       6    8    0    7
+    8 a       7    9    0    8
+    9 a       8   10    0    9
+   10 G       9   11    6   10
+   11 G      10   12    5   11
+   12 G      11   13    4   12
+   13 C      12   14    3   13
+   14 C      13   15    2   14
+   15 C      14    0    1   15
diff -r 000000000000 -r 07b6202d71e2 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 17 16:49:04 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="rnastructure" version="5.7">
+		<repository changeset_revision="455b68271b2b" name="package_rnastructure_5_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+	</package>
+</tool_dependency>