diff export2graphlan.xml @ 0:cac6247cb1d3 draft

graphlan_import

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export2graphlan.xml	Tue Aug 26 14:51:29 2014 -0400
@@ -0,0 +1,85 @@
+<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::
+
+----
+
+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>