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comparison text-from-interval.xml @ 2:014a21767ac4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:57 -0400
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1:ae9994cf526f 2:014a21767ac4
1 <?xml version="1.0"?>
2 <tool id="circos_interval_to_text" name="Circos: Interval to Circos Text Labels" version="@WRAPPER_VERSION@">
3 <description>reformats interval files to prepare for Circos text labels</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[
10 python
11 #if $ref.ref_source == 'gff3':
12 '$__tool_directory__/text-from-gff3.py' '$input' '${ref.attr}'
13 #else
14 '$__tool_directory__/text-from-bed.py' '$input'
15 #end if
16 > '$output'
17 ]]></command>
18 <inputs>
19 <conditional name="ref">
20 <param name="ref_source" type="select" label="Data Format">
21 <option value="bed" selected="true">BED6+</option>
22 <option value="gff3">GFF3</option>
23 </param>
24 <when value="bed">
25 <param name="input" type="data" format="bed" label="BED File (BED6+ only)" />
26 </when>
27 <when value="gff3">
28 <param name="input" type="data" format="gff3" label="GFF3 File" />
29 <param name="attr" type="text" label="GFF3 Attribute to pull value from" />
30 </when>
31 </conditional>
32 </inputs>
33 <outputs>
34 <data name="output" format="tabular" />
35 </outputs>
36 <tests>
37 <test>
38 <conditional name="ref">
39 <param name="ref_source" value="bed" />
40 <param name="input" value="text/1.bed" ftype="bed" />
41 </conditional>
42 <output name="output" file="text/1.out" ftype="tabular" />
43 </test>
44 <test>
45 <conditional name="ref">
46 <param name="ref_source" value="gff3" />
47 <param name="input" value="text/2.gff3" ftype="gff3" />
48 <param name="attr" value="Name" />
49 </conditional>
50 <output name="output" file="text/2.out" ftype="tabular" />
51 </test>
52 </tests>
53 <help><![CDATA[
54 Converts standard BED6+ and GFF3 files into a format appropriate for Circos data tracks, especially text tracks.
55
56 BED3 files cannot be used as they lack the name field.
57 ]]></help>
58 <expand macro="citations" />
59 </tool>