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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:22:05 -0400
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1 <tool id="FastQC" name="FastQC" version="1.0.0">
2 <description>quality control checks on raw sequence data</description>
3 <command interpreter="python">fastqc.py
4 #if $input.extension.startswith( "fastq"):
5 --format=fastq
6 #else
7 --format=$input.extension
8 #end if
9 --input='$input'
10 --name='$input.name'
11 --dir='$report.extra_files_path'
12 --report='$report'
13 #if $contaminants != None and $contaminants != "None" and $contaminants != "":
14 --contaminants=$contaminants
15 #end if
16 </command>
17 <inputs>
18 <param name="input" type="data" format="fastq,sam,bam" label="FASTQ reads" />
19 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminants"
20 help="Two fields per line separated by a TAB: name DNA_sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/>
21 </inputs>
22 <outputs>
23 <data name="report" format="html" />
24 </outputs>
25 <tests>
26 <!--
27 <test>
28 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
29 <output name="output1_file" file="split_pair_reads_1.fastqsanger" />
30 <output name="output2_file" file="split_pair_reads_2.fastqsanger" />
31 </test>
32 -->
33 </tests>
34 <help>
35 **What it does**
36
37 FastQC_ is a product of Bioinformatics Group at the Babraham Institute. FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
38
39 The main functions of FastQC are::
40
41 - Import of data from BAM, SAM or FastQ files (any variant)
42 - Provding a quick overview to tell you in which areas there may be problems
43 - Summary graphs and tables to quickly assess your data
44 - Export of results to an HTML based permanent report
45 - Offline operation to allow automated generation of reports without running the interactive application
46
47
48 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
49
50 -----
51
52 **Input format**
53
54 Any fastq file, for example::
55
56 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
57 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
58 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
59 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
60
61 **Contaminants format**
62
63 An optional contaminant file (otherwise FastQC will use the default)::
64
65 # This file contains a list of potential contaminants which are
66 # frequently found in high throughput sequencing reactions. These
67 # are mostly sequences of adapters / primers used in the various
68 # sequencing chemistries.
69 #
70 # You can add more sequences to the file by putting one line per entry
71 # and specifying a name[tab]sequence. If the contaminant you add is
72 # likely to be of use to others please consider sending it to the FastQ
73 # authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
74 # or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
75 # the program can benefit.
76 Illumina Single End Apapter 1 ACACTCTTTCCCTACACGACGCTGTTCCATCT
77 Illumina Single End Apapter 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
78 Illumina Single End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
79 Illumina Single End PCR Primer 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
80 Illumina Single End Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT
81
82
83 -----
84
85 **Outputs**
86
87 An HTML file with links to::
88
89 - fastqc_report.html
90 - summary.txt
91 - fastqc_data.txt
92
93 </help>
94 </tool>