Mercurial > repos > rnateam > veinnarna_rnaplot

annotate rnaplot.xml @ 0:aa3b07e8c3ec draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
author rnateam
date Wed, 05 Oct 2016 04:59:34 -0400
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aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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1 <tool id="veinnarna_rnaplot" name="@EXECUTABLE@" version="@VERSION@.0">
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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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 < '$input'
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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13 --layout-type=$layoutSelector
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14 --output-format=$formatOptions.formatSelector
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15 #if str($formatOptions.formatSelector) == "ps"
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16 --pre=$formatOptions.pre
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17 --post=$formatOptions.post
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18 && tar -cf '$imagesFile' *.ps
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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19 #elif str($formatOptions.formatSelector) == "gml"
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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20 && tar -cf '$imagesFile' *.gml
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21 #elif str($formatOptions.formatSelector) == "svg"
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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22 && tar -cf '$imagesFile' *.svg
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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23 #else
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24 && tar -cf '$imagesFile' *.ss
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25 #end if
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26 ]]>
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27 </command>
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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28 <inputs>
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29 <param format="txt,dbn" name="input" type="data" label="DotBracket structure"/>
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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30 <param name="layoutSelector" type="select" label="Layout selection" argument="--layout-type">
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31 <option value="0">Radial Layout</option>
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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">
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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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>
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37 <option value="gml">Graph Meta Language (.gml)</option>
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38 <option value="svg">Scalable Vector Graphics (.svg)</option>
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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"/>
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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
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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82 ------
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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83
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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84 **Outputs**
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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85
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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86 - several possible postscript images bundled together in a tar file
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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87
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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88
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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89 ]]>
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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90 </help>
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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91 <expand macro="citations" />
aa3b07e8c3ec planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit d1bef7f37f272e3173c137fcb690364fee7e6d1f
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92 </tool>