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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
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5 -i "$input_file"
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6 -d "$html_file.files_path"
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7 -o "$html_file"
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8 -t "$text_file"
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9 -n "$out_prefix"
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10 -f "$input_file.ext"
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11 -j "$input_file.name"
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12 -e "\$FASTQC_JAR_PATH/fastqc"
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13 #if $contaminants.dataset and str($contaminants) > ''
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14 -c "$contaminants"
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15 #end if
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16 #if $limits.dataset and str($limits) > ''
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17 -l "$limits"
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18 #end if
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19 </command>
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20 <requirements>
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21 <requirement type="package" version="0.11.2">FastQC</requirement>
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22 </requirements>
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23 <inputs>
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24 <param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" />
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25 <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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26 help="Letters and numbers only please - other characters will be removed">
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27 <sanitizer invalid_char="">
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28 <valid initial="string.letters,string.digits"/>
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29 </sanitizer>
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30 </param>
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31 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
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32 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/>
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33 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
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34 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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35 </inputs>
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36 <outputs>
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37 <data format="html" name="html_file" label="${out_prefix}_${input_file.name}_Webpage.html" />
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38 <data format="txt" name="text_file" label="${out_prefix}_${input_file.name}_RawData.txt" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_file" value="1000gsample.fastq" />
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43 <param name="out_prefix" value="fastqc_out" />
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44 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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45 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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46 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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47 </test>
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48 <test>
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49 <param name="input_file" value="1000gsample.fastq" />
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50 <param name="out_prefix" value="fastqc_out" />
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51 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
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52 <output name="html_file" file="fastqc_report2.html" ftype="html" lines_diff="100"/>
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53 <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="100"/>
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54 </test>
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55 </tests>
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56 <help>
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57
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58 .. class:: infomark
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59
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60 **Purpose**
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61
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62 FastQC aims to provide a simple way to do some quality control checks on raw
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63 sequence data coming from high throughput sequencing pipelines.
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64 It provides a modular set of analyses which you can use to give a quick
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65 impression of whether your data has any problems of
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66 which you should be aware before doing any further analysis.
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67
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68 The main functions of FastQC are:
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69
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70 - Import of data from BAM, SAM or FastQ files (any variant)
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71 - Providing a quick overview to tell you in which areas there may be problems
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72 - Summary graphs and tables to quickly assess your data
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73 - Export of results to an HTML based permanent report
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74 - Offline operation to allow automated generation of reports without running the interactive application
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75
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76
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77 -----
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78
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79
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80 .. class:: infomark
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81
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82 **FastQC**
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83
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84 This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_
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85 Kindly acknowledge it as well as this tool if you use it.
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86 FastQC incorporates the Picard-tools_ libraries for sam/bam processing.
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87
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88 The contaminants file parameter was borrowed from the independently developed
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89 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.
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90 Adaption to version 0.11.2 by T. McGowan.
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91
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92 -----
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93
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94 .. class:: infomark
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95
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96 **Inputs and outputs**
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97
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98 FastQC_ is the best place to look for documentation - it's very good.
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99 A summary follows below for those in a tearing hurry.
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100
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101 This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check.
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102 It will also take an optional file containing a list of contaminants information, in the form of
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103 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
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104 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
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105 which modules to include in the output.
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106
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107 The tool produces a basic text and a HTML output file that contain all of the results, including the following:
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108
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109 - Basic Statistics
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110 - Per base sequence quality
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111 - Per sequence quality scores
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112 - Per base sequence content
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113 - Per base GC content
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114 - Per sequence GC content
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115 - Per base N content
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116 - Sequence Length Distribution
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117 - Sequence Duplication Levels
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118 - Overrepresented sequences
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119 - Kmer Content
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120
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121 All except Basic Statistics and Overrepresented sequences are plots.
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122 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
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123 .. _Picard-tools: http://picard.sourceforge.net/index.shtml
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124
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125 </help>
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126 <citations>
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127 <citation type="bibtex">
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128 @ARTICLE{andrews_s,
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129 author = {Andrews, S.},
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130 keywords = {bioinformatics, ngs, qc},
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131 priority = {2},
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132 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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133 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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134 }
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135 </citation>
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136 </citations>
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137 </tool>
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