--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export2graphlan.xml	Wed Apr 20 06:09:29 2016 -0400
@@ -0,0 +1,215 @@
+<tool id="export2graphlan" name="Export to GraPhlAn" version="0.19">
+
+    <description></description>
+
+    <requirements>
+        <requirement type="package" version="0.16">pandas</requirement>
+        <requirement type="package" version="0.16">scipy</requirement>
+        <requirement type="package" version="1.4">matplotlib</requirement>
+        <requirement type="package" version="0.19">export2graphlan</requirement>
+    </requirements>
+
+    <stdio>
+    </stdio>
+
+    <version_command>
+<![CDATA[
+export2graphlan.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+        export2graphlan.py
+            -i $lefse_input
+
+            #if $lefse_output
+                -o lefse_output
+            #end if
+
+            -t $tree
+            -a $annotation
+
+            #if $annotations
+                --annotations $annotations
+            #end if
+
+            #if $external_annotations
+                --external_annotations $external_annotations
+            #end if
+
+            #if $background_levels
+                --background_levels $background_levels
+            #end if
+
+            #if $background_clades
+                --background_clades "$background_clades"
+            #end if
+
+            #if $background_colors
+                --background_colors "$background_colors"
+            #end if
+ 
+            #if $title
+                --title "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
+                --most_abundant $most_abundant
+            #end if
+
+            #if $least_biomarkers
+                --least_biomarkers $least_biomarkers
+            #end if
+
+            --fname_row $fname_row
+            --sname_row $sname_row
+
+            #if $metadata_rows
+                --metadata_rows $metadata_rows
+            #end if
+                  
+            #if $skip_rows  
+                --skip_rows $skip_rows
+            #end if
+
+            #if $sperc
+                --sperc $sperc
+            #end if
+
+            #if $fperc
+                --fperc $fperc
+            #end if
+
+            #if $stop
+                --stop $stop
+            #end if
+
+            #if $ftop
+                --ftop $ftop
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="lefse_input" type="data" format="tabular,txt,tsv" label="Input file" help="Identical to LEfSe input file (--lefse_input)"/>
+
+        <param name="lefse_output" type="data" format="tabular" label="Input file corresponding to LEfSe output file (Optional)" help="(--lefse_output)" optional="True"/>
+
+        <param name="annotations" type="text" label="List which levels should be annotated in the tree (Optional)" help="The levels must be in comma-separated form (--annotations)" optional="True"/>
+
+        <param name="external_annotations" type="text" label="List which levels should use the external legend for the annotation (Optional)" help="The levels must be in comma-separated form (--external_annotations)" optional="True"/>
+
+        <param name="background_levels" type="text" label="List which levels should be highlight with a shaded background (Optional)" help="The levels must be in comma-separated form (--background_levels)" optional="True"/>
+
+        <param name="background_clades" type="text" label="List of the clades that should be highlight with a shaded background (Optional)" help="The clades must be in comma-separated form (--background_clades)" optional="True"/>
+
+        <param name="background_colors" type="text" label="List of color to use for the shaded background (Optional)" help="Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()). The different colors must be in comma-separated form (--background_colors)" optional="True"/>
+        
+        <param name="title" type="text" label="Title of the GraPhlAn plot (Optional)" help="(--title)" optional="True"/>
+
+        <param name="title_font_size" type="integer" value="15" label="Title font size" help="(--title_font_size)"/>
+
+        <param name="def_clade_size" type="integer" value="10" label="Default size for clades that are not found as biomarkers" help="(--def_clade_size)"/>
+
+        <param name="min_clade_size" type="integer" value="20" label="Minimum value of clades that are biomarkers" help="(--min_clade_size)"/>
+
+        <param name="max_clade_size" type="integer" value="200" label="Maximum value of clades that are biomarkers" help="(--max_clade_size)"/>
+
+        <param name="def_font_size" type="integer" value="10" label="Default font size" help="(--def_font_size)"/>
+
+        <param name="min_font_size" type="integer" value="8" label="Minimum font size" help="(--min_font_size)"/>
+
+        <param name="max_font_size" type="integer" value="12" label="Maximum font size" help="(--max_font_size)"/>
+
+        <param name="annotation_legend_font_size" type="integer" value="10" label="Font size for the annotation legend" help="(--annotation_legend_font_size)"/>
+
+        <param name="abundance_threshold" type="float" value="20.0" label="Minimun abundance value for a clade to be annotated" help="(--abundance_threshold)"/>
+
+        <param name="most_abundant" type="integer" label="Number of clades to highlight (Optional)" help="(--most_abundant)" optional="True"/>
+
+        <param name="least_biomarkers" type="integer" label="Minimum number of biomarkers to extract (Optional)" help=" The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers(--least_biomarkers)" optional="True"/>
+
+        <param name="fname_row" type="integer" value="0" label="Row number containing the names of the features" help="-1 specifies that no names are present in the matrix (--fname_row)"/>
+
+        <param name="sname_row" type="integer" value="0" label="Row number containing the names of the samples" help="-1 specifies that no names are present in the matrix (--sname_row)"/>
+
+        <param name="metadata_rows" type="integer" label="Row number to use as metadata (Optional)" help="(--metadata_rows)" optional="True"/>
+
+        <param name="skip_rows" type="text" label="Row number to skip from the input file" help="The row numbers ar indexed to 0 and comma separated (--skip_rows)" optional="True"/>
+
+        <param name="sperc" type="float" label="Percentile of sample value 
+            distribution for sample selection (Optional)" help="(--sperc)" 
+            optional="True"/>
+
+        <param name="fperc" type="float" label="Percentile of feature value distribution for sample selection (Optional)" help="(--fperc)" optional="True"/>
+
+        <param name="stop" type="integer" label="Number of top samples to select (Optional)" help="The order is based on percentile specified by --sperc (--stop)" optional="True"/>
+
+        <param name="ftop" type="integer" label="Number of top features to select (Optional)" help="The order is based on percentile specified by --fperc (--ftop)" optional="True"/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="tree" label="${tool.name} on ${on_string}: Tree" />
+        <data format="txt" name="annotation" label="${tool.name} on ${on_string}: Annotation" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="lefse_input" value="input_profile.tabular"/>
+            <param name="annotations" value=""/>
+            <param name="external_annotations" value=""/>
+            <param name="background_levels" value=""/>
+            <param name="background_clades" value=""/>
+            <param name="background_colors" value=""/>
+            <param name="title" value=""/>
+            <param name="title_font_size" value="15"/>
+            <param name="def_clade_size" value="10"/>
+            <param name="min_clade_size" value="20"/>
+            <param name="max_clade_size" value="200"/>
+            <param name="def_font_size" value="10"/>
+            <param name="min_font_size" value="8"/>
+            <param name="max_font_size" value="12"/>
+            <param name="annotation_legend_font_size" value="10"/>
+            <param name="abundance_threshold" value="20.0"/>
+            <param name="most_abundant" value=""/>
+            <param name="least_biomarkers" value=""/>
+            <param name="fname_row" value="0"/>
+            <param name="sname_row" value="0" />
+            <param name="metadata_rows" value=""/>
+            <param name="skip_rows" value=""/>
+            <param name="sperc" value=""/>
+            <param name="fperc" value=""/>
+            <param name="stop" value=""/>
+            <param name="ftop" value=""/>
+            <output name="annotation" file="annotation_output.txt"/>
+            <output name="tree" file="tree_output.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. It can convert MetaPhlAn, LEfSe, and/or HUMAnN output to GraPhlAn input format
+
+In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. 
+
+For more information, check the 
+`user manual <https://bitbucket.org/CibioCM/export2graphlan/overview/>`_.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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