Mercurial > repos > jjohnson > fastqc
annotate fastqc/fastqc.xml @ 0:1d373f219445 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:22:05 -0400 |
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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> |