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annotate graphlan.xml @ 0:c5746c07ca5e draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
author bebatut
date Mon, 01 Feb 2016 07:45:14 -0500
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children 5cdaa98d9376
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c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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1 <tool id="graphlan" name="GraPhlAn" version="0.1.0">
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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2
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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3 <description>to produce graphical output of an input tree</description>
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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4
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5 <requirements>
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6 <requirement type="package" version="1.66">biopython</requirement>
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7 <requirement type="package" version="1.4">matplotlib</requirement>
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8 <requirement type="package" version="1.0">graphlan</requirement>
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9 </requirements>
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10
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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11 <stdio>
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12 </stdio>
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13
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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14 <version_command>
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15 <![CDATA[
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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16 python \${GRAPHLAN_DIR}/graphlan.py -v
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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17 ]]>
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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18 </version_command>
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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19
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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20 <command>
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21 <![CDATA[
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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22 python \${GRAPHLAN_DIR}/graphlan.py
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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23 --format $format
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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24
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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25 #if $dpi
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26 --dpi $dpi
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27 #end if
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28
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29 --size $size
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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30
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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31 #if $pad
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32 --pad $pad
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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33 #end if
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34
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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35 $input_tree
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36
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37 #if str($format) == "png"
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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38 $png_output_image
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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39 #else if str($format) == "pdf"
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40 $pdf_output_image
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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41 #else if str($format) == "ps"
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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42 $ps_output_image
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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43 #else if str($format) == "eps"
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44 $eps_output_image
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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45 #else
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46 $svg_output_image
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47 #end if
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48 ]]>
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49 </command>
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50
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51 <inputs>
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52 <param name="input_tree" type="data" format="txt" label="Input tree in
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53 PhlyloXML format" help=""/>
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54
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55 <param name='format' type="select" label="Output format"
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56 help="(--format)">
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57 <option value="png" selected="true">PNG</option>
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58 <option value="pdf">PDF</option>
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59 <option value="ps">PS</option>
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60 <option value="eps">EPS</option>
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61 <option value="svg">SVG</option>
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62 </param>
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63
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64 <param name="dpi" type="integer" label="Dpi of the output image
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65 (Optional)" help="For non vectorial formats (--dpi)" optional="True"/>
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66
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67 <param name="size" type="integer" value="7" label="Size of the output image
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68 (in inches)" help="(--size)"/>
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69
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70 <param name="pad" type="integer" label="Distance between the most external
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71 graphical element and the border of the image (Optional)"
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72 help="(--pad)" optional="True"/>
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73 </inputs>
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74
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75 <outputs>
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76 <data format="png" name="png_output_image"
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77 label="${tool.name} on ${on_string}: Image">
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78 <filter>format=="png"</filter>
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79 </data>
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80 <data format="pdf" name="pdf_output_image"
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81 label="${tool.name} on ${on_string}: Image">
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82 <filter>format=="pdf"</filter>
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83 </data>
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84 <data format="ps" name="ps_output_image"
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85 label="${tool.name} on ${on_string}: Image">
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86 <filter>format=="ps"</filter>
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87 </data>
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88 <data format="eps" name="eps_output_image"
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89 label="${tool.name} on ${on_string}: Image">
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90 <filter>format=="eps"</filter>
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91 </data>
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92 <data format="svg" name="svg_output_image"
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93 label="${tool.name} on ${on_string}: Image">
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94 <filter>format=="svg"</filter>
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95 </data>
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96 </outputs>
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97
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98 <tests>
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99 <test>
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100 </test>
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101 </tests>
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102
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103 <help><![CDATA[
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104
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105 **What it does**
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106
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107 GraPhlAn is a software tool for producing high-quality circular
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108 representations of taxonomic and phylogenetic trees. GraPhlAn focuses on
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109 concise, integrative, informative, and publication-ready representations of
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110 phylogenetically- and taxonomically-driven investigation.
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111
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112 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
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113
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114 ]]></help>
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115
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116 <citations>
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117 </citations>
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118 </tool>