Mercurial > repos > bgruening > viennarna_rnaplot

annotate rnaplot.xml @ 0:1d249ed33108 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
author bgruening
date Wed, 05 Oct 2016 11:52:23 -0400
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1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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1 <tool id="viennarna_rnaplot" name="@EXECUTABLE@" version="@VERSION@.0">
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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2 <description> Draw RNA Secondary Structures </description>
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3 <macros>
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4 <token name="@EXECUTABLE@">RNAplot</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 RNAplot < '$input'
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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13 --layout-type=$layoutSelector
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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14 --output-format=$formatOptions.formatSelector
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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15 #if str($formatOptions.formatSelector) == "ps"
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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16 --pre=$formatOptions.pre
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17 --post=$formatOptions.post
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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18 && tar -cf '$imagesFile' *.ps
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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19 #elif str($formatOptions.formatSelector) == "gml"
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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20 && tar -cf '$imagesFile' *.gml
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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21 #elif str($formatOptions.formatSelector) == "svg"
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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22 && tar -cf '$imagesFile' *.svg
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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23 #else
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24 && tar -cf '$imagesFile' *.ss
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25 #end if
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26 ]]>
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27 </command>
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28 <inputs>
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29 <param format="txt,dbn" name="input" type="data" label="DotBracket structure"/>
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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30 <param name="layoutSelector" type="select" label="Layout selection" argument="--layout-type">
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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31 <option value="0">Radial Layout</option>
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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32 <option value="1" selected="true">Naview Layout</option>
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33 </param>
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34 <conditional name="formatOptions">
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35 <param name="formatSelector" type="select" label="Output format selection" help="--output-format">
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36 <option value="ps" selected="true">Postscript (.ps)</option>
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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37 <option value="gml">Graph Meta Language (.gml)</option>
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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38 <option value="svg">Scalable Vector Graphics (.svg)</option>
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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39 <option value="xrna">XRNA Save File (.ss)</option>
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40 </param>
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41 <when value="ps">
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42 <param name="pre" type="text" label="Add annotation macros to postscript file" help="--pre"/>
1d249ed33108 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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43 <param name="post" type="text" label="Add annotations to postscript file" help="--post"/>
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44 </when>
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45 <when value="gml">
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46 </when>
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47 <when value="svg">
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48 </when>
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49 <when value="xrna">
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50 </when>
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51 </conditional>
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52 </inputs>
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53
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54 <outputs>
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55 <data format="tar" name="imagesFile"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="input" value="rnaplot_input1.dbn"/>
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60 <output name="imagesFile">
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61 <assert_contents>
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62 <has_line line="%%Title: RNA Secondary Structure Plot"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help>
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68 <![CDATA[
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69
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70 **RNAplot**
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71
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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.
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73
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74 -----
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75
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76 **Input format**
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77
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78 RNAplot requires one input file
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79
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80 - Fasta file with an additional line with structure information in dot-bracket notation
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81
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82 ------
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83
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84 **Outputs**
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85
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86 - several possible postscript images bundled together in a tar file
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87
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89 ]]>
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90 </help>
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91 <expand macro="citations" />
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92 </tool>