view import2graphlan.xml @ 59:000d65b33ecd draft

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<tool id="import2graphlan" name="import2graphlan" version="1.0.0">
  <description>Import to Graphlan</description>
  <command  interpreter="python">
    export2graphlan.py 
	-i $inp_data 
	-o $out_data
	-t $output_tree_file 
	-a $output_annot_file 

	--annotations $export_annotations 
	--external_annotations $export_external_annotations
	--background_levels  $background_levels 


	#if $str($gchoice.global_choice)  == "a":

		#if $str($gchoice.background_clades)  != " ":
		       	--background_clades  $gchoice.background_clades
		#end if
		#if $str($gchoice.background_colors)  != " ":
		       	--background_colors  $gchoice.background_colors
		#end if

		#if $str($gchoice.export_title)  != " ":
		       	--title $gchoice.export_title
		#end if




		--title_font_size  $gchoice.title_font_size 
		--def_clade_size  $gchoice.def_clade_size 
		--min_clade_size  $gchoice.min_clade_size 
		--max_clade_size  $gchoice.max_clade_size 
		--def_font_size  $gchoice.def_font_size 
		--min_font_size  $gchoice.min_font_size 
		--max_font_size  $gchoice.max_font_size 
		--annotation_legend_font_size $gchoice.annotation_legend_font_size
		--abundance_threshold $gchoice.abundance_threshold
		--least_biomarkers $gchoice.least_biomarkers 

		#if $str($gchoice.discard_otus )  == "1":
		       	  --discard_otus 
		#end if	 
	#end if

	

	--skip_rows 1,2 
   </command>
   
   <inputs>
		<param format="tabular" name="inp_data" type="data" label="Input used to run Lefse" 	help="This is the file that was used as input for Lefse"/>
		<param format="lefse_internal_res" name="out_data" type="data" label="Output of  Lefse"  help="This is the  Lefse output file"/>	
	   	<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 name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>  
		
		<conditional name="gchoice">       
			<param name="global_choice" type="select" label="Select Global Choices" help="Select choices">
				<option value="d" selected='True'>Default</option>
		  		<option value="a">Advanced</option>
			</param>
			<when value="d">
				<param name="background_clades" type="hidden" format="text" label="Background Clades" value="" />  
			</when> 
			<when value="a">
				<param name="background_clades" type="text" format="text" label="Background Clades" value=" " />  
				<param name="background_colors" type="text" format="text" label="Background Colors" value=" " />  
			    	<param name="export_title" type="text" format="text" label="Title" value=" "/>
			    	<param name="title_font_size"  type="integer" size="4" value="15"   label="Title font size"/>
			    	<param name="def_clade_size"  type="integer" size="4" value="0"   label="Default Clade size"/>
			    	<param name="min_clade_size"  type="integer" size="4" value="20"   label="Minimum Clade size that are Biomarkers"/>
			    	<param name="max_clade_size"  type="integer" size="4" value="200"   label="Maximum Clade size that are Biomarkers"/>
			    	<param name="def_font_size"  type="integer" size="4" value="10"   label="Default font size"/>
			    	<param name="min_font_size"  type="integer" size="4" value="8"   label="Minimum font size "/>
			    	<param name="max_font_size"  type="integer" size="4" value="12"   label="Maximum font size "/>
			    	<param name="annotation_legend_font_size"  type="integer" size="4" value="10"   label="Annotation legend font size "/>
			    	<param name="abundance_threshold"  type="float"   value="20.0"   label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
			    	<param name="most_abundant"  type="integer" size="4" value="0"   label=" When only lefse_input is provided, you can specify how many clades to highlight "/>
				<param name="least_biomarkers"  type="integer" size="4" value="0"   label="Minimum number of biomarkers to extract  "/>
				<param name="discard_otus" type="select" label="If specified the OTU ids will be discarded from the taxonomy" value="0" >
						<option value="0">No</option>
						<option value="1">Yes</option>
				</param>
			</when>
		 </conditional>
    </inputs>
   <outputs>
            <data  name="output_annot_file"  format="circl"  />
            <data  name="output_tree_file"  format="circl"  />
   </outputs>
                                  
  <help>
Overview
========
**export2graphlan** is an *OPTIONAL* tool that automatically convert **LEfSe**, **MetaPhlAn2**, and **HUMAnN** input and/or output files, to **GraPhlAn**. Input file can be also given in BIOM (both 1 and 2) format.

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

Input files
===========

As shown in the image below, export2graphlan can work with just one of the following files or with both of them.

 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value.

 * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers.

Input parameters 
================
 
    **--annotations** ANNOTATIONS List which levels should be annotated in the tree. Use a comma separate values form, e.g., -annotation_levels 1,2,3. Default is None
 
 
    **--external_annotations** EXTERNAL_ANNOTATIONS   List which levels should use the external legend for the annotation. Use a comma separate values form, e.g., --annotation_levels 1,2,3. Default is None


    **--background_levels** BACKGROUND_LEVELS   List which levels should be highlight with a shaded background. Use a comma separate values form, e.g.,--background_levels 1,2,3 


    **--background_clades** BACKGROUND_CLADES
                        Specify the clades that should be highlight with a  shaded background. Use a comma separate values form and surround the string with " if it contains spaces.

                        Example: --background_clades "Bacteria.Actinobacteria,Bacteria.Bacteroidetes.Bacteroidia,Bacteria.Firmicutes.Clostridia.Clostridiales"


    **--background_colors** BACKGROUND_COLORS   Set the color to use for the shaded background. Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()) format. 

			Use a comma separate values form and surround the string with " if it contains spaces. 	Example:  #29cc36, (150; 100; 100), (280;80; 88)


    **--title TITLE**   If specified set the title of the GraPhlAn plot. Surround the string with " if it contains spaces, e.g., --title "Title example" 

    **--title_font_size** TITLE_FONT_SIZE    Set the title font size. Default is 15


    **--def_clade_size** DEF_CLADE_SIZE   Set a default size for clades that are not found as biomarkers by LEfSe. Default is 10


    **--min_clade_size** MIN_CLADE_SIZE  Set the minimum value of clades that are biomarkers. Default is 20


    **--max_clade_size** MAX_CLADE_SIZE Set the maximum value of clades that are biomarkers.  Default is 200


    **--def_font_size**  DEF_FONT_SIZE  Set a default font size. Default is 10


    **--min_font_size** MIN_FONT_SIZE Set the minimum font size to use. Default is 8


    **--max_font_size** MAX_FONT_SIZE Set the maximum font size. Default is 12


    **--annotation_legend_font_size**  ANNOTATION_LEGEND_FONT_SIZE Set the font size for the annotation legend. Default is 10

    **--abundance_threshold**  ABUNDANCE_THRESHOLD  Set the minimun abundace value for a clade to be annotated. Default is 20.0


    **--most_abundant**  MOST_ABUNDANT When only lefse_input is provided, you can specify how many clades highlight. Since the biomarkers are missing, they will be chosen from the most abundant


    **--least_biomarkers**  LEAST_BIOMARKERS   When only lefse_input is provided, you can specify the minimum number of biomarkers to extract. The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers


    **--discard_otus**     If specified the OTU ids will be discarded from the taxonmy. Default behavior keep OTU ids in taxonomy

    **--internal_levels**   If specified sum-up from leaf to root the abundances values. Default behavior do not sum-up abundances on the internal nodes

  
Input data matrix parameters
============================

    **--sep** SEP

    **--out_table** OUT_TABLE   : This is where to write the  processed data matrix to file

    **--fname_row** FNAME_ROW   :  Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix)

    **--sname_row** SNAME_ROW     column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)

    **--metadata_rows** METADATA_ROWS   Row numbers to use as metadata[default None, meaning no metadata

    **--skip_rows** SKIP_ROWS  Row numbers to skip (0-indexed, comma separated) from the input file[default None, meaning no rows skipped 

    **--sperc** SPERC         Percentile of sample value distribution for sample selection

    **--fperc** FPERC         Percentile of feature value distribution for sample selection

    **--stop** STOP           Number of top samples to select (ordering based on percentile specified by --sperc)

    **--ftop** FTOP           Number of top features to select (ordering based on percentile specified by --fperc)

    **--def_na** DEF_NA       Set the default value for missing values [default None which means no replacement]

Integration
===========

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

.. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png
    :height: 672
    :width: 800

Want to know more?
==================

If you want to know more about **export2graphlan** please have a look at the tutorial  `here`_


.. _here:  https://bitbucket.org/nsegata/graphlan/wiki/export2graphlan%20-%20tutorial
  </help>
</tool>