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
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"
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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"
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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"
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3 <requirements>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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4 <requirement type="package" version="1.0">cgview</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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16 -show_sequence_features $show_sequence_features
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17 -sequence '${reference}'
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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18 -blast '${blast_output}'
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19 -output '${output}'
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20 ]]>
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21 </command>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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22 <inputs>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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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"
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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"
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25 <param name="gc_skew" type="boolean" truevalue="T" falsevalue="F" label="Display GC Skew" checked="false" help=""/>
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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"
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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"
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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"
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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"
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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"
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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=""/>
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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"
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33 </inputs>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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34 <outputs>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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35 <data name="output" format="xml"/>
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36 </outputs>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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37 <tests>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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38 </tests>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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39 <help>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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40 </help>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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41 <citations>
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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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"
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43 @article{
a3b4d4c9bd51 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
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44 stothard2004circular,
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45 title={Circular genome visualization and exploration using CGView},
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46 author={Stothard, Paul and Wishart, David S},
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47 journal={Bioinformatics},
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48 volume={21},
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49 number={4},
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50 pages={537--539},
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51 year={2004},
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52 publisher={Oxford University Press}
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53 }
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54 </citation>
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55 </citations>
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56 </tool>