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1 <tool id="export2graphlan" name="export2graphlan" version="1.0.0">
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2 <description>Export to Graphlan</description>
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3 <command interpreter="python">
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4 export2graphlan.py
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5 -i $inp_data
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6 -o $out_data
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7 -t $output_tree_file
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8 -a $output_annot_file
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9 --title $export_title
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10 --annotations $export_annotations
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11 --external_annotations $export_external_annotations
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12 --skip_rows 1,2
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13 </command>
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14
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15 <inputs>
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16 <param name="export_title" type="text" format="text" label="Title" value="Title"/>
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17 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
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18 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>
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19 <param format="tabular" name="inp_data" type="data" label="Input used to run Lefse - See samples below - Please use Galaxy Get-Data/Upload-File. Use File-Type = Tabular" help="This is the file that was used as input for Lefse"/>
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20 <param format="lefse_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/>
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21 </inputs>
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22 <outputs>
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23 <data name="output_annot_file" format="circl" />
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24 <data name="output_tree_file" format="circl" />
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25 </outputs>
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26
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27 <help>
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28 **export2graphlan** is an automatic conversion script from **LEfSe**, **MetaPhlAn2**, and **HUMAnN** input and/or output files, to **GraPhlAn**. Input file can be also given in BIOM 2.0 format.
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29
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30 The aim of this tool is to support biologists, helping them by automatically write the tree and the annotation file for **GraPhlAn**.
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31
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32 ----
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33
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34 .. contents::
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35
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36 ----
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37
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38 Overview
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39 ========
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40
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41 A graphical representation of how **export2graphlan** can be used in the analysis pipeline:
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42
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43 .. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png
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44 :height: 500
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45 :width: 600
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46
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47
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48 ----
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49
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50 HMP aerobiosis
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51 ==============
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52
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53 A taxonomic tree that shows three different classes of oxygen (low, medium, and high), highlighting biomarker clades for each class. Data are taken from the HMP project.
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54
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55 .. image:: https://bitbucket.org/repo/oL6bEG/images/2487320460-hmp_aerobiosis.png
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56 :height: 500
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57 :width: 600
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58
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59
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60 Pipeline
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61 --------
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62
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63
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64 # download the data
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65 $ wget http://huttenhower.sph.harvard.edu/webfm_send/129 -O hmp_aerobiosis_small.txt
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66
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67 # convert the file in LEfSe format, and run LEfSe
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68 $ format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000
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69 $ run_lefse.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res
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70
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71 # convert it!
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72 $ export2graphlan.py -i hmp_aerobiosis_small.txt -o hmp_aerobiosis_small.res -t tree.txt -a annot.txt --title "HMP aerobiosis" --annotations 2,3 --external_annotations 4,5,6 --fname_row 0 --skip_rows 1,2 --ftop 200
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73
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74 # attach annotation to the tree
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75 $ graphlan_annotate.py --annot annot.txt tree.txt outtree.txt
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76
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77 # generate the beautiful image
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78 $ graphlan.py --dpi 300 --size 7.0 outtree.txt outimg.png --external_legends
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79
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80 The input file is downloaded from The Huttenhower Lab and given to **LEfSe** for biomarkers discovery. The two file (the *LEfSe input* and the *LEfSe output* files) are then passed to **export2graphlan**. In this case the levels 2 (*phylum*) and 3 (*class*) are annotated on the circular tree, while levels 4 (*order*), 5 (*family*), and 6 (*genus*) are put on the external legend.
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81
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82
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83
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84 </help>
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85 </tool>
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