Mercurial > repos > bgruening > dot2ct
changeset 0:07b6202d71e2 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author | bgruening |
---|---|
date | Thu, 17 Sep 2015 16:49:04 -0400 |
parents | |
children | |
files | dot2ct.xml test-data/example1_input.dot-bracket.txt test-data/example1_output_seq1.ct.txt tool_dependencies.xml |
diffstat | 4 files changed, 68 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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 +((((((...))).))
--- /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
--- /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>