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annotate dot2ct.xml @ 0:07b6202d71e2 draft default tip

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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
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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2 <tool id="rnastructure_dot2ct" name="Dot-Bracket to Connect Table (CT)" version="5.7.a">
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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3 <description>Converts the first sequence in a Dot-Bracket file into a CT file</description>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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4 <requirements>
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5 <requirement type="package" version="5.7">rnastructure</requirement>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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6 </requirements>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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7
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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8 <version_command>dot2ct --version | grep -i version</version_command>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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9
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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10 <command>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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11 dot2ct
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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12 $dotbracket_structure
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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13 $ct_structure
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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14 </command>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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15
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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16 <inputs>
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17 <param format="dbn" name="dotbracket_structure" type="data" label="Alignment in BAM or SAM format" />
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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18 </inputs>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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19
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20 <outputs>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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21 <data format="txt" name="ct_structure" label="${tool.name} on ${dotbracket_structure.name}" />
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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22 </outputs>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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23
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24 <tests>
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25 <test>
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26 <param name="dotbracket_structure" value="example1_input.dot-bracket.txt" format="dbn" />
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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27
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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28 <output name="ct_structure" file="example1_output_seq1.ct.txt" />
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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29 </test>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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30 </tests>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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32 <help>Convert a Dot-Bracket file into a Connect Table.</help>
07b6202d71e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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34 <citations>
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35 <citation type="doi">10.1186/1471-2105-11-129</citation>
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36 </citations>
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37 </tool>