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author schang
date Tue, 02 Dec 2014 19:53:37 -0500
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1 <tool id="frp_tool" name="Fragment Recruitment Plot">
2 <description>for SAM outputs</description>
3 <requirements>
4 <requirement type="python-module">matplotlib.pyplot</requirement>
5 </requirements>
6 <command interpreter="python">frp_tool.py -i $identity -b $begin -l $length -t "$title" -m "$microbiome" -c $color $input $ref_genome $out_file</command>
7 <inputs>
8 <param name="input" type="data" format="sam" label="Dataset" help="Dataset missing? See help below"/>
9 <param name="ref_genome" type="data" format="fasta" label="Reference Genome"/>
10 <param name="identity" type="integer" value="50" max="100" label="Percent Identity" help="Minimum identity to include in plot (y-axis extent)"/>
11 <param name="begin" type="integer" value="0" label="Begin plot at the nth nucleotide of reference genome"/>
12 <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"/>
13 <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."/>
14 <param name="microbiome" type="text" size="30" value="Human Skin" label="Microbiome Description" help="Optional subtitle"/>
15 <param name="color" type="select" label="Point Color" help="Color for plot points">
16 <option value="0">Dark Gold</option>
17 <option value="1">Light Orange</option>
18 <option value="2">Light Green</option>
19 <option value="3">Fuschia</option>
20 <option value="4">Medium Blue</option>
21 <option value="5">Light Plum</option>
22 </param>
23 </inputs>
24 <outputs>
25 <data format="png" name="out_file" from_work_dir="frp_image.png"/>
26 </outputs>
27
28 <tests>
29 <test>
30 <param name="input" value="frp_input.sam"/>
31 <param name="ref_genome" value="genomic.fasta"/>
32 <param name="identity" value="50"/>
33 <param name="begin" value="0"/>
34 <param name="length" value="0"/>
35 <param name="title" value=""/>
36 <param name="microbiome" value=""/>
37 <param name="color" value="Light Green"/>
38 <output name="out_file" file="frp_output.png"/>
39 </test>
40 </tests>
41
42 <help>
43 **What it does**
44
45 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.
46
47 ------
48
49 **Input Datasets/Files**
50
51 Two input types are required in this tool:
52
53 1. Reference genome: the reference sequence in FASTA format used for alignment; it can be uploaded via Get Data -> Upload File.
54
55 2. SAM format dataset: can be uploaded via Get Data -> Upload File. It can also be obtained after alignment with Bowtie2.
56
57 If using Bowtie2 output, follow these steps to format the file properly:
58
59 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
60
61 2. Use these options in the samtool_filter2:
62 + Exclude Header
63 + Minimum MAPQ quality score = 1
64
65 .. class:: infomark
66
67 **TIP:** This ensures the file contains all aligned reads without any missing MD tags per line.
68
69 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
70
71 ------
72
73 **Output Example**
74
75 An example image (png format) of a fragment recruitment plot.
76
77 .. image:: ${static_path}/images/frp_output_small.png
78
79
80
81 </help>
82
83 </tool>