Mercurial > repos > dfornika > cgview_xml_builder
annotate cgview_xml_builder.xml @ 0:a3b4d4c9bd51 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
author | dfornika |
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date | Thu, 12 Dec 2019 19:32:56 +0000 |
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a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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1 <tool id="cgview_xml_builder" name="cgview XML builder" version="1.0+galaxy0"> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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2 <description>Circular Genome Viewer</description> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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3 <requirements> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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4 <requirement type="package" version="1.0">cgview</requirement> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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5 </requirements> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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6 <command detect_errors="exit_code"> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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7 <![CDATA[ |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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8 cgview_xml_builder.pl |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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9 -gc_content $gc_content |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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10 -gc_skew $gc_skew |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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11 -at_content $at_content |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
parents:
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12 -at_skew $at_skew |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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13 -average $average |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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14 -feature_labels $feature_labels |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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15 -use_opacity $use_opacity |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
parents:
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16 -show_sequence_features $show_sequence_features |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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17 -sequence '${reference}' |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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18 -blast '${blast_output}' |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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19 -output '${output}' |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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20 ]]> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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21 </command> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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22 <inputs> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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23 <param name="reference" type="data" format="genbank,fasta" label="Reference" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
parents:
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24 <param name="gc_content" type="boolean" truevalue="T" falsevalue="F" label="Display GC Content" checked="true" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
parents:
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25 <param name="gc_skew" type="boolean" truevalue="T" falsevalue="F" label="Display GC Skew" checked="false" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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26 <param name="at_content" type="boolean" truevalue="T" falsevalue="F" label="Display AT Content" checked="false" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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27 <param name="at_skew" type="boolean" truevalue="T" falsevalue="F" label="Display AT Skew" checked="false" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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28 <param name="average" type="boolean" truevalue="T" falsevalue="F" label="Display deviation of GC and AT values from the average for the entire genome." checked="true" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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29 <param name="feature_labels" type="boolean" truevalue="T" falsevalue="F" label="Display feature labels from GenBank file" checked="false" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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30 <param name="use_opacity" type="boolean" truevalue="T" falsevalue="F" label="Draw BLAST hits with partial opacity" checked="false" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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31 <param name="show_sequence_features" type="boolean" truevalue="T" falsevalue="F" label="Draw features in the reference (GenBank) file" checked="false" help=""/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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32 <param name="blast_output" type="data" format="tabular" /> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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33 </inputs> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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34 <outputs> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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35 <data name="output" format="xml"/> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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36 </outputs> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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37 <tests> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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38 </tests> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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39 <help> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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40 </help> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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41 <citations> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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42 <citation type="bibtex"> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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43 @article{ |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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44 stothard2004circular, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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45 title={Circular genome visualization and exploration using CGView}, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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46 author={Stothard, Paul and Wishart, David S}, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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47 journal={Bioinformatics}, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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48 volume={21}, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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49 number={4}, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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50 pages={537--539}, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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51 year={2004}, |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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52 publisher={Oxford University Press} |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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53 } |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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54 </citation> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
dfornika
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55 </citations> |
a3b4d4c9bd51
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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56 </tool> |