Mercurial > repos > george-weingart > graphlan_import

changeset 22:b43531754e71 draft

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author george-weingart
date Thu, 04 Sep 2014 16:42:59 -0400
parents 5ecece9f42dd
children 01ba9f83f9a7
files export2graphlan.xml
diffstat 1 files changed, 0 insertions(+), 202 deletions(-) [+]
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--- a/export2graphlan.xml	Thu Sep 04 16:34:51 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
-<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 
-
-	--annotations $export_annotations 
-	--external_annotations $export_external_annotations
-	--background_levels  $background_levels 
-	#if $str($background_clades)  != " ":
-               	--background_clades  $background_clades
-	#end if
-	#if $str($background_colors)  != " ":
-               	--background_colors  $background_colors
-	#end if
-	#if $str($export_title)  != " ":
-               	--title $export_title
-	#end if
-	--title_font_size  $title_font_size 
-	--def_clade_size  $def_clade_size 
-	--min_clade_size  $min_clade_size 
-	--max_clade_size  $max_clade_size 
-	--def_font_size  $def_font_size 
-	--min_font_size  $min_font_size 
-	--max_font_size  $max_font_size 
-        --annotation_legend_font_size $annotation_legend_font_size
-	--abundance_threshold $abundance_threshold
-	#if  $most_abundant  > 0:
-               	--most_abundant  $most_abundant
-	#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"/>   
-		<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 "/>
-
-   least_biomarkers
-    </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:
-                        --background_colors "#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 discarde 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 parameters:
-
-    -i LEFSE_INPUT, --lefse_input LEFSE_INPUT 
-                   
-    -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT
-
-    output parameters:
-
-    -t TREE, --tree TREE  Output filename where save the input tree for GraPhlAn
-
-    -a ANNOTATION, --annotation ANNOTATION :  This is the Output filename where to save GraPhlAn annotation
-  
-    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
-  </help>
-</tool>