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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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1d373f219445 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="FastQC" name="FastQC" version="1.0.0">
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2 <description>quality control checks on raw sequence data</description>
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3 <command interpreter="python">fastqc.py
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4 #if $input.extension.startswith( "fastq"):
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5 --format=fastq
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6 #else
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7 --format=$input.extension
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8 #end if
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9 --input='$input'
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10 --name='$input.name'
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11 --dir='$report.extra_files_path'
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12 --report='$report'
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13 #if $contaminants != None and $contaminants != "None" and $contaminants != "":
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14 --contaminants=$contaminants
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15 #end if
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16 </command>
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17 <inputs>
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18 <param name="input" type="data" format="fastq,sam,bam" label="FASTQ reads" />
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19 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminants"
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20 help="Two fields per line separated by a TAB: name DNA_sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/>
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21 </inputs>
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22 <outputs>
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23 <data name="report" format="html" />
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24 </outputs>
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25 <tests>
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26 <!--
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27 <test>
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28 <param name="input1_file" value="3.fastqsanger" ftype="fastqsanger" />
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29 <output name="output1_file" file="split_pair_reads_1.fastqsanger" />
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30 <output name="output2_file" file="split_pair_reads_2.fastqsanger" />
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31 </test>
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32 -->
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33 </tests>
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34 <help>
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35 **What it does**
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36
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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.
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38
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39 The main functions of FastQC are::
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40
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41 - Import of data from BAM, SAM or FastQ files (any variant)
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42 - Provding a quick overview to tell you in which areas there may be problems
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43 - Summary graphs and tables to quickly assess your data
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44 - Export of results to an HTML based permanent report
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45 - Offline operation to allow automated generation of reports without running the interactive application
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46
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47
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48 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
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49
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50 -----
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51
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52 **Input format**
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53
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54 Any fastq file, for example::
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55
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56 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
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57 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
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58 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
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59 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
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60
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61 **Contaminants format**
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62
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63 An optional contaminant file (otherwise FastQC will use the default)::
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64
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65 # This file contains a list of potential contaminants which are
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66 # frequently found in high throughput sequencing reactions. These
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67 # are mostly sequences of adapters / primers used in the various
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68 # sequencing chemistries.
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69 #
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70 # You can add more sequences to the file by putting one line per entry
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71 # and specifying a name[tab]sequence. If the contaminant you add is
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72 # likely to be of use to others please consider sending it to the FastQ
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73 # authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
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74 # or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
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75 # the program can benefit.
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76 Illumina Single End Apapter 1 ACACTCTTTCCCTACACGACGCTGTTCCATCT
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77 Illumina Single End Apapter 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
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78 Illumina Single End PCR Primer 1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
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79 Illumina Single End PCR Primer 2 CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
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80 Illumina Single End Sequencing Primer ACACTCTTTCCCTACACGACGCTCTTCCGATCT
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81
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82
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83 -----
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84
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85 **Outputs**
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86
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87 An HTML file with links to::
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88
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89 - fastqc_report.html
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90 - summary.txt
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91 - fastqc_data.txt
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92
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93 </help>
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94 </tool>