Mercurial > repos > bebatut > graphlan

annotate graphlan_annotate.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_annotate" name="Modify an input tree for GraPhlAn" version="0.1.0">
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3 <description></description>
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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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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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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[
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16 python \${GRAPHLAN_DIR}/graphlan_annotate.py -v
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17 ]]>
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18 </version_command>
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20 <command>
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21 <![CDATA[
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22 python \${GRAPHLAN_DIR}/graphlan_annotate.py
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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23 #if $annot
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24 --annot $annot
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25 #end if
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27 $input_tree
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28 $output_tree
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29 ]]>
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30 </command>
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32 <inputs>
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33 <param name="input_tree" type="data" format="txt" label="Input tree"
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34 help="Newick, Nexus, PhyloXML or plain text"/>
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36 <param name="annot" type="data" format="txt" label="Annotation file
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37 (Optional)" help="(--annot)" optional="True"/>
c5746c07ca5e planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/graphlan/ commit c1077b92ffc7d750e04fd327f32caca7a9bb2a2a-dirty
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38 </inputs>
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40 <outputs>
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41 <data format="text" name="output_tree"
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42 label="${tool.name} on ${on_string}: Tree in PhyloXML" />
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43 </outputs>
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45 <tests>
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46 <test>
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47 </test>
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48 </tests>
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50 <help><![CDATA[
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51
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52 **What it does**
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53
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54 GraPhlAn is a software tool for producing high-quality circular
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55 representations of taxonomic and phylogenetic trees. GraPhlAn focuses on
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56 concise, integrative, informative, and publication-ready representations of
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57 phylogenetically- and taxonomically-driven investigation.
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58
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59 `graphlan_annotate` modifies any input tree (in any of the three standard format)
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60 adding additional information regarding structural or graphical aspects of the tree
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61 (like colors and style of the taxa, labels, shadows, heatmaps, ...).
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62
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63 For more information, check the `user manual <https://bitbucket.org/nsegata/graphlan/overview>`_.
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64
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65 ]]></help>
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66
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67 <citations>
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68 </citations>
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69 </tool>