comparison export2graphlan.xml @ 0:cac6247cb1d3 draft

graphlan_import

0:cac6247cb1d3

<tool id="export2graphlan" name="export2graphlan" version="1.0.0">
  <description>Export to Graphlan</description>
  <command  interpreter="python">
    export2graphlan.py 
	-i $inp_data 
	-o $out_data
	-t $output_tree_file 
	-a $output_annot_file 
	--title $export_title
	--annotations $export_annotations 
	--external_annotations $export_external_annotations
	--skip_rows 1,2 
   </command>
   
	<inputs>
	    <param name="export_title" type="text" format="text" label="Title" value="Title"/>
	    <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
	    <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>   
		<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"/>
		<param format="lefse_res" name="out_data" type="data" label="Output of  Lefse"  help="This is the  Lefse output file"/>	
    </inputs>
	<outputs>
            <data  name="output_annot_file"  format="circl"  />
            <data  name="output_tree_file"  format="circl"  />
	</outputs>
                                  
  <help>
**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.

The aim of this tool is to support biologists, helping them by automatically write the tree and the annotation file for **GraPhlAn**.

----

.. contents::

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Overview
========

A graphical representation of how **export2graphlan** can be used in the analysis pipeline:

.. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png
    :height: 500   
    :width: 600 
 

----

HMP aerobiosis
==============

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.

.. image:: https://bitbucket.org/repo/oL6bEG/images/2487320460-hmp_aerobiosis.png
    :height: 500   
    :width: 600 
 

Pipeline
--------

 
    # download the data
    $ wget http://huttenhower.sph.harvard.edu/webfm_send/129 -O hmp_aerobiosis_small.txt

    # convert the file in LEfSe format, and run LEfSe
    $ format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000
    $ run_lefse.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res

    # convert it!
    $ 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

    # attach annotation to the tree
    $ graphlan_annotate.py --annot annot.txt tree.txt outtree.txt

    # generate the beautiful image
    $ graphlan.py --dpi 300 --size 7.0 outtree.txt outimg.png --external_legends

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.
 


  </help>
</tool>