<tool id="frp_tool" name="Fragment Recruitment Plot">
  <description>for SAM outputs</description>
  <requirements>
  	<requirement type="python-module">matplotlib.pyplot</requirement>
  </requirements>
  <command interpreter="python">frp_tool.py -i $identity -b $begin -l $length -t "$title" -m "$microbiome" -c $color $input $ref_genome $out_file</command>
  <inputs>
    <param name="input" type="data" format="sam"  label="Dataset" help="Dataset missing? See help below"/>
    <param name="ref_genome" type="data" format="fasta" label="Reference Genome"/>
    <param name="identity" type="integer" value="50" max="100" label="Percent Identity" help="Minimum identity to include in plot (y-axis extent)"/>
    <param name="begin" type="integer" value="0" label="Begin plot at the nth nucleotide of reference genome"/>
    <param name="length" type="integer" value="0" label="Include n nucleotides on the x-axis of the plot" help="Default to 0 for full length"/>
    <param name="title" type="text" size="30" value="E. coli" label="Plot Title" help="(e.g. name of the reference genome). Default is the accession number of reference genome."/>
    <param name="microbiome" type="text" size="30" value="Human Skin" label="Microbiome Description" help="Optional subtitle"/>
    <param name="color" type="select" label="Point Color" help="Color for plot points">
    	<option value="0">Dark Gold</option>
    	<option value="1">Light Orange</option>
    	<option value="2">Light Green</option>
    	<option value="3">Fuschia</option>
    	<option value="4">Medium Blue</option> 
    	<option value="5">Light Plum</option>
    </param>
  </inputs>
  <outputs>
    <data format="png" name="out_file" from_work_dir="frp_image.png"/>
  </outputs>

  <tests>
    <test>
      <param name="input" value="frp_input.sam"/>
      <param name="ref_genome" value="genomic.fasta"/>
      <param name="identity" value="50"/>
      <param name="begin" value="0"/>
      <param name="length" value="0"/>
      <param name="title" value=""/>
      <param name="microbiome" value=""/>
      <param name="color" value="Light Green"/>
      <output name="out_file" file="frp_output.png"/>
    </test>
  </tests>

  <help>
**What it does**

This tool creates a fragment recruitment plot from a SAM input file. Its main purpose is to display a graph of aligned metagenomic reads against an organism's reference genome. The percent identity is calculated based on the MD: tag in the optional form field of the SAM format.

------

**Input Datasets/Files**

Two input types are required in this tool:

1. Reference genome: the reference sequence in FASTA format used for alignment; it can be uploaded via Get Data -> Upload File.
	
2. SAM format dataset: can be uploaded via Get Data -> Upload File. It can also be obtained after alignment with Bowtie2.
	 
If using Bowtie2 output, follow these steps to format the file properly:
	
1. Filter the BAM/SAM output from Bowtie2 by executing the "samtool_filter2" tool from the Tool Shed. More information can be found in this link: http://toolshed.g2.bx.psu.edu/view/devteam/samtool_filter2
	
2. Use these options in the samtool_filter2: 
	+ Exclude Header
	+ Minimum MAPQ quality score = 1
		
	.. class:: infomark
	
	**TIP:** This ensures the file contains all aligned reads without any missing MD tags per line.
		
3. Convert BAM-to-SAM by using using the tool "bam_to_sam" installed from the Tool Shed. Additional information can be found in this link:: http://toolshed.g2.bx.psu.edu/view/devteam/bam_to_sam

------

**Output Example**

An example image (png format) of a fragment recruitment plot.

.. image:: ${static_path}/images/frp_output_small.png


	
  </help>

</tool>