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1 <tool name="FastQC:Read QC" id="fastqc" version="0.62">
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2 <description>reports using FastQC</description>
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3 <command interpreter="python">
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4 rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -t "$text_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_JAR_PATH/fastqc"
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5 #if $contaminants.dataset and str($contaminants) > ''
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6 -c "$contaminants"
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7 #end if
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8 #if $limits.dataset and str($limits) > ''
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9 -l "$limits"
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10 #end if
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11 </command>
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12 <requirements>
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13 <requirement type="package" version="0.11.2">FastQC</requirement>
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14 </requirements>
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15 <inputs>
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16 <param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" />
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17 <param name="out_prefix" value="FastQC" type="text" label="Title for the output file - to remind you what the job was for" size="80"
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18 help="Letters and numbers only please - other characters will be removed">
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19 <sanitizer invalid_char="">
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20 <valid initial="string.letters,string.digits"/>
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21 </sanitizer>
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22 </param>
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23 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
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24 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/>
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25 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
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26 help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
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27 </inputs>
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28 <outputs>
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29 <data format="html" name="html_file" label="${out_prefix}_${input_file.name}_Webpage.html" />
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30 <data format="txt" name="text_file" label="${out_prefix}_${input_file.name}_RawData.txt" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input_file" value="1000gsample.fastq" />
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35 <param name="out_prefix" value="fastqc_out" />
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36 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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37 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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38 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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39 </test>
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40 <test>
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41 <param name="input_file" value="1000gsample.fastq" />
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42 <param name="out_prefix" value="fastqc_out" />
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43 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
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44 <output name="html_file" file="fastqc_report2.html" ftype="html" lines_diff="100"/>
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45 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="100"/>
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46 </test>
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47 </tests>
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48 <help>
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49
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50 .. class:: infomark
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51
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52 **Purpose**
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53
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54 FastQC aims to provide a simple way to do some quality control checks on raw
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55 sequence data coming from high throughput sequencing pipelines.
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56 It provides a modular set of analyses which you can use to give a quick
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57 impression of whether your data has any problems of
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58 which you should be aware before doing any further analysis.
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59
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60 The main functions of FastQC are:
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61
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62 - Import of data from BAM, SAM or FastQ files (any variant)
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63 - Providing a quick overview to tell you in which areas there may be problems
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64 - Summary graphs and tables to quickly assess your data
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65 - Export of results to an HTML based permanent report
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66 - Offline operation to allow automated generation of reports without running the interactive application
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67
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68
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69 -----
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70
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71
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72 .. class:: infomark
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73
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74 **FastQC**
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75
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76 This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_
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77 Kindly acknowledge it as well as this tool if you use it.
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78 FastQC incorporates the Picard-tools_ libraries for sam/bam processing.
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79
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80 The contaminants file parameter was borrowed from the independently developed
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81 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.
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82 Adaption to version 0.11.2 by T. McGowan.
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83
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84 -----
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85
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86 .. class:: infomark
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87
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88 **Inputs and outputs**
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89
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90 FastQC_ is the best place to look for documentation - it's very good.
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91 A summary follows below for those in a tearing hurry.
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92
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93 This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check.
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94 It will also take an optional file containing a list of contaminants information, in the form of
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95 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
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96 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
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97 which modules to include in the output.
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98
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99 The tool produces a basic text and a HTML output file that contain all of the results, including the following:
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100
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101 - Basic Statistics
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102 - Per base sequence quality
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103 - Per sequence quality scores
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104 - Per base sequence content
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105 - Per base GC content
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106 - Per sequence GC content
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107 - Per base N content
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108 - Sequence Length Distribution
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109 - Sequence Duplication Levels
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110 - Overrepresented sequences
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111 - Kmer Content
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112
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113 All except Basic Statistics and Overrepresented sequences are plots.
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114 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
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115 .. _Picard-tools: http://picard.sourceforge.net/index.shtml
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116
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117 </help>
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118 </tool>
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