Mercurial > repos > iuc > graphlan

annotate graphlan.xml @ 2:6e8eb0c0d91f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit fb23555b3087ca4022f0d186dfea40c2407ca211
author iuc
date Fri, 09 Feb 2024 21:29:49 +0000
parents a490b70e46fc
children
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a490b70e46fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit b5bd1ab6e4f3a14819dbc2bdad33006bc6131b3c"
iuc
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1 <tool id="graphlan" name="GraPhlAn" version="@WRAPPER_VERSION@">
0
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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2 <description>to produce graphical output of an input tree</description>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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3 <macros>
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4 <import>graphlan_macros.xml</import>
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5 </macros>
2
6e8eb0c0d91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit fb23555b3087ca4022f0d186dfea40c2407ca211
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <stdio>
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9 <regex match="Warning"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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10 source="stderr"
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11 level="warning"
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12 description="" />
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13 </stdio>
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14 <version_command>graphlan.py -v</version_command>
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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15 <command>
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16 <![CDATA[
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17 graphlan.py
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18 --format '$image_format.format'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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19 --size '$size'
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20 #if $pad
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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21 --pad '$pad'
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22 #end if
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23 #if str($image_format.format) == "png" and $image_format.dpi
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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24 --dpi '$image_format.dpi'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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25 #end if
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26 '$input_tree'
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27 #if str($image_format.format) == "png"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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28 '$png_output_image'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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29 #else if str($image_format.format) == "pdf"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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30 '$pdf_output_image'
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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31 #else if str($image_format.format) == "ps"
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32 '$ps_output_image'
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33 #else if str($image_format.format) == "eps"
8f62f666dcb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit 6e73e77d186e02d200fc3a61d25311e67864a824
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34 '$eps_output_image'
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35 #else
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36 '$svg_output_image'
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37 #end if
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param name="input_tree" type="data" format="txt,nhx,phyloxml" label="Input tree"/>
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42 <conditional name="image_format">
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43 <param argument='--format' type="select" label="Output format">
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44 <option value="png" selected="true">PNG</option>
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45 <option value="pdf">PDF</option>
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46 <option value="ps">PS</option>
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47 <option value="eps">EPS</option>
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48 <option value="svg">SVG</option>
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49 </param>
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50 <when value="png">
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51 <param argument="--dpi" type="integer" label="Dpi of the output image" optional="True"/>
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52 </when>
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53 <when value="pdf"/>
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54 <when value="ps"/>
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55 <when value="eps"/>
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56 <when value="svg"/>
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57 </conditional>
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58 <param argument="--size" type="integer" value="7" label="Size of the output image"/>
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59 <param argument="--pad" type="integer" label="Distance between the most external graphical element and the border of the image" optional="True"/>
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60 </inputs>
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61 <outputs>
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62 <data format="png" name="png_output_image" label="${tool.name} on ${on_string}: PNG">
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63 <filter>image_format['format']=="png"</filter>
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64 </data>
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65 <data format="pdf" name="pdf_output_image" label="${tool.name} on ${on_string}: PDF">
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66 <filter>image_format['format']=="pdf"</filter>
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67 </data>
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68 <data format="ps" name="ps_output_image" label="${tool.name} on ${on_string}: PS">
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69 <filter>image_format['format']=="ps"</filter>
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70 </data>
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71 <data format="eps" name="eps_output_image" label="${tool.name} on ${on_string}: EPS">
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72 <filter>image_format['format']=="eps"</filter>
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73 </data>
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74 <data format="svg" name="svg_output_image" label="${tool.name} on ${on_string}: SVG">
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75 <filter>image_format['format']=="svg"</filter>
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76 </data>
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77 </outputs>
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78 <tests>
2
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79 <test expect_num_outputs="1">
0
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80 <param name="input_tree" value="intermediary_tree"/>
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81 <param name="format" value="png"/>
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82 <param name="dpi" value="100"/>
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83 <param name="size" value="7"/>
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84 <param name="pad" value="2"/>
1
a490b70e46fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/ commit b5bd1ab6e4f3a14819dbc2bdad33006bc6131b3c"
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85 <output name="png_output_image" file="png_image.png" compare="sim_size" delta="20000"/>
0
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89 **What it does**
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90
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91 GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
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92
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93 For more information, check the `user manual <https://github.com/biobakery/graphlan>`_.
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94
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95 ]]></help>
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96 <expand macro="citations"/>
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97 </tool>