--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/home/ubuntu/lefse_to_export/plot_features.xml	Wed Aug 20 16:56:51 2014 -0400
@@ -0,0 +1,159 @@
+<tool id="LEfSe_fea" name="F) Plot Differential Features" version="1.0">
+  <description></description>
+<command interpreter="python">plot_features.py  $inp_data $inp_res $arch --title_font_size $graphical.title_font_size --background_color $graphical.background_color --class_label_pos $graphical.class_label_pos --class_font_size $graphical.class_font_size --top $graphical.top --bot $graphical.bot --font_size $graphical.font_size --width $graphical.width --height $graphical.height -f $feature_set  --archive "zip" --format $for --dpi $dpi --subcl_mean $graphical.subcl_mean --subcl_median $graphical.subcl_median </command>  
+  <inputs>
+    <page>
+	<param format="lefse_internal_for" name="inp_data" type="data" label="The formatted datasets" help=""/>
+	<param format="lefse_internal_res" name="inp_res" type="data" label="The LEfSe output" help=""/>
+
+	<param name="feature_set" type="select" label="Do you want to plot all features or only those detected as biomarkers?">
+		<option value="diff" selected="diff">Biomarkers only</option>
+		<option value="all">All</option>
+	</param> 
+
+
+	<conditional name="graphical">
+	<param name="graphical_choice" type="select" label="Set some graphical options to personalize the output">
+                        <option value="d" selected='True'>Default</option>
+                        <option value="a">Advanced</option>
+	</param>
+       	<when value="d">
+		<param name="top" type="hidden" value="-1.0" />
+		<param name="bot" type="hidden" value="0.0" />
+                <param name="title_font_size" type="hidden" value="14" />
+                <param name="class_font_size" type="hidden" value="12" />
+                <param name="font_size" type="hidden" value="8" />
+                <param name="width" type="hidden" value="7.0" />
+                <param name="height" type="hidden" value="4.0" />
+                <param name="background_color" type="hidden" value="w" />
+		<param name="width" type="hidden" value="7.0" />
+                <param name="height" type="hidden" value="4.0" />
+		<param name="class_label_pos" type="hidden" value="up" />
+		<param name="subcl_mean" type="hidden" value="y" />
+		<param name="subcl_median" type="hidden" value="y" />
+	</when>
+
+	<when value="a">
+		<param name="top" type="float" size="2" value="-1.0" label="Set the maximum y value (-1.0 means automatic maximum setting based on maximum class median)"/>
+		<param name="bot" type="float" size="2" value="0.0" label="Set the minimum y value (-1.0 means automatic minimum setting based on minimum class median)"/>
+		<param name="title_font_size" type="integer" size="2" value="14" label="Title font size"/>
+	        <param name="class_font_size" type="integer" size="2" value="12" label="Class font size"/>
+	        <param name="font_size" type="integer" size="2" value="8" label="Size of subclasses names and y values"/>
+	        <param name="width" type="float" size="2" value="7.0" label="Width of the plot"/>
+	        <param name="height" type="float" size="2" value="4.0" label="Height of the plot"/>
+		<param name="background_color" type="select" label="Background color">
+			<option value="w" selected='True'>White</option>
+                        <option value="k">Black</option>
+                </param>
+		<param name="class_label_pos" type="select" label="Class label position">
+			<option value="up" selected='True'>Top</option>
+                        <option value="down">Bottom</option>
+                </param>
+		<param name="subcl_mean" type="select" label="Whether to plot the subclass means (straight line)">
+                        <option value="y" selected='True'>Yes</option>
+                        <option value="n">No</option>
+                </param>
+		<param name="subcl_median" type="select" label="Whether to plot the subclass medians (dotted line)">
+                        <option value="y" selected='True'>Yes</option>
+                        <option value="n">No</option>
+                </param>
+
+        </when>
+
+        </conditional>		
+
+    	<param name="for" type="select" label="Output format">
+                <option value="png" selected="png">png</option>
+                <option value="svg">svg</option>
+                <option value="pdf">pdf</option>
+        </param>
+        <param name="dpi" type="select" label="Set the dpi resolution of the output">
+                <option value="72">72</option>
+                <option value="150" selected="True">150</option>
+                <option value="300">300</option>
+                <option value="600">600</option>
+                <option value="1200">1200</option>
+        </param>
+
+	</page>
+   </inputs>
+  <outputs>
+    <data format="zip" name="arch" >
+     </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/>
+      <param name="maf_source" value="cached"/>
+      <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/>
+      <param name="species" value="hg18,mm8"/>
+      <param name="overwrite_with_gaps" value="True"/>
+      <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
+      <param name="maf_source" value="cached"/>
+      <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/>
+      <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
+      <param name="overwrite_with_gaps" value="True"/>
+      <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
+      <param name="maf_source" value="user"/>
+      <param name="maf_file" value="5.maf"/>
+      <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
+      <param name="overwrite_with_gaps" value="True"/>
+      <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" />
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+This module plots the raw data of the features detected by LEfSe as biomarkers as abundance histograms
+with class and subclass information. The features are exported as images and
+the user can download all the images in a .zip archive. It is also possible to
+export all the features (instead of the biomarkers only). For exporting or
+analyzing few features only the "Plot One Feature" module is recommended. 
+
+------
+
+**Input format**
+
+The module accepts two datasets: the data formatted with the "Format Input for
+LEfSe" module and the output of the LEfSe analysis. Both datasets are necessary
+to run the module.
+
+------
+
+**Output format**
+
+The module generates zip archives containing images in png, svg or pdf format. 
+
+------
+
+**Advanced parameter settings**
+                
+*Graphical options*
+        * Set the maximum y value: -1 means automatic parameter setting that is computed as the minimum between the highest abundance value and three times the highest subclass median.
+        * Set the minimum y value: -1 means automatic parameter setting that is computed as the maximum between 0 and the 90% of the smallest abundance value.
+        * Title font size: set the font size of the title only.
+        * Class font size: set the font of the legend for the class names and colors.
+        * Size of subclasses names and y values: set the font size for the axis labels.
+        * Width of the plot: horizontal size (in inches) of the plot.
+        * Height of the plot: vertical size (in inches) of the plot.
+        * Background color: whether to generate plots with black or white backgrounds, adjusting properly the other colors.
+        * Class label position: whether to place the class labels on the top or on the bottom of the plot.
+        * Plot subclass means (straight line): whether to plot the subclass means with straight horizontal lines.
+        * Plot subclass medians (dotted line): whether to plot the subclass medians with dotted horizontal lines.
+
+------
+
+**Examples**
+
+Please see the examples reported for the "Plot One Feature" module (E). This
+module just produces multiple plots in the same way and compresses them into a
+.zip archive. 
+
+  </help>
+</tool>