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+++ b/frp_tool.xml	Tue Dec 02 19:53:37 2014 -0500
@@ -0,0 +1,83 @@
+<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>
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