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