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comparison rnaplot.xml @ 0:b64631260c13 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author rnateam
date Tue, 06 Dec 2016 12:34:05 -0500
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1 <tool id="viennarna_rnaplot" name="@EXECUTABLE@" version="@VERSION@.0">
2 <description> Draw RNA Secondary Structures </description>
3 <macros>
4 <token name="@EXECUTABLE@">RNAplot</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 RNAplot < '$input'
13 --layout-type=$layoutSelector
14 --output-format=$formatOptions.formatSelector
15 #if str($formatOptions.formatSelector) == "ps"
16 --pre=$formatOptions.pre
17 --post=$formatOptions.post
18 && tar -cf '$imagesFile' *.ps
19 #elif str($formatOptions.formatSelector) == "gml"
20 && tar -cf '$imagesFile' *.gml
21 #elif str($formatOptions.formatSelector) == "svg"
22 && tar -cf '$imagesFile' *.svg
23 #else
24 && tar -cf '$imagesFile' *.ss
25 #end if
26 ]]>
27 </command>
28 <inputs>
29 <param format="txt,dbn" name="input" type="data" label="DotBracket structure"/>
30 <param name="layoutSelector" type="select" label="Layout selection" argument="--layout-type">
31 <option value="0">Radial Layout</option>
32 <option value="1" selected="true">Naview Layout</option>
33 </param>
34 <conditional name="formatOptions">
35 <param name="formatSelector" type="select" label="Output format selection" help="--output-format">
36 <option value="ps" selected="true">Postscript (.ps)</option>
37 <option value="gml">Graph Meta Language (.gml)</option>
38 <option value="svg">Scalable Vector Graphics (.svg)</option>
39 <option value="xrna">XRNA Save File (.ss)</option>
40 </param>
41 <when value="ps">
42 <param name="pre" type="text" label="Add annotation macros to postscript file" help="--pre"/>
43 <param name="post" type="text" label="Add annotations to postscript file" help="--post"/>
44 </when>
45 <when value="gml">
46 </when>
47 <when value="svg">
48 </when>
49 <when value="xrna">
50 </when>
51 </conditional>
52 </inputs>
53
54 <outputs>
55 <data format="tar" name="imagesFile"/>
56 </outputs>
57 <tests>
58 <test>
59 <param name="input" value="rnaplot_input1.dbn"/>
60 <output name="imagesFile">
61 <assert_contents>
62 <has_line line="%%Title: RNA Secondary Structure Plot"/>
63 </assert_contents>
64 </output>
65 </test>
66 </tests>
67 <help>
68 <![CDATA[
69
70 **RNAplot**
71
72 The program reads RNA sequences and structures in the format as produced by RNAfold and produces drawings of the secondary structure graph. The coordinates are produced using either E. Bruccoleri's naview routines, or a simple radial layout method.
73
74 -----
75
76 **Input format**
77
78 RNAplot requires one input file
79
80 - Fasta file with an additional line with structure information in dot-bracket notation
81
82 ------
83
84 **Outputs**
85
86 - several possible postscript images bundled together in a tar file
87
88
89 ]]>
90 </help>
91 <expand macro="citations" />
92 </tool>