<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>