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annotate rgFastQC.xml @ 8:5b995cef2fbb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit bff04a5409662a8968c50501487042a3a0c93702
author iuc
date Tue, 31 Jan 2017 07:22:22 -0500
parents ec73b7c83b2c
children 0a7c65540937
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1 <tool id="fastqc" name="FastQC" version="0.67">
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2 <description>Read Quality reports</description>
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3 <requirements>
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4 <requirement type="package" version="0.11.5">fastqc</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 <exit_code range=":-1" />
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9 <regex match="Error:" />
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10 <regex match="Exception:" />
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11 </stdio>
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12 <command><![CDATA[
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13 python '${__tool_directory__}/rgFastQC.py'
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14 -i '$input_file'
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15 -d '${html_file.files_path}'
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16 -o '$html_file'
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17 -t '$text_file'
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18 -f '${input_file.ext}'
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19 -j '${input_file.name}'
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20 #if $contaminants.dataset and str($contaminants) > ''
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21 -c '$contaminants'
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22 #end if
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23 #if $limits.dataset and str($limits) > ''
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24 -l '$limits'
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25 #end if
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26 ]]></command>
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27 <inputs>
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28 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data" label="Short read data from your current history" />
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29 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
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30 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />
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31 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
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32 help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
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33 </inputs>
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34 <outputs>
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35 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
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36 <data format="txt" name="text_file" label="${tool.name} on ${on_string}: RawData" />
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="input_file" value="1000gsample.fastq" />
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41 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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42 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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43 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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44 </test>
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45 <test>
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46 <param name="input_file" value="1000gsample.fastq" />
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47 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
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48 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
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49 <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
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50 </test>
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51 <test>
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52 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
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53 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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54 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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55 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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56 </test>
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57 <test>
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58 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
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59 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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60 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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61 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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62 </test>
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63 </tests>
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64 <help>
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65 .. class:: infomark
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66
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67 **Purpose**
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68
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69 FastQC aims to provide a simple way to do some quality control checks on raw
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70 sequence data coming from high throughput sequencing pipelines.
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71 It provides a modular set of analyses which you can use to give a quick
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72 impression of whether your data has any problems of
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73 which you should be aware before doing any further analysis.
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74
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75 The main functions of FastQC are:
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76
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77 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
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78 - Providing a quick overview to tell you in which areas there may be problems
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79 - Summary graphs and tables to quickly assess your data
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80 - Export of results to an HTML based permanent report
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81 - Offline operation to allow automated generation of reports without running the interactive application
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82
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83 -----
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84
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85 .. class:: infomark
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86
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87 **FastQC**
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88
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89 This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_
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90 Kindly acknowledge it as well as this tool if you use it.
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91 FastQC incorporates the Picard-tools_ libraries for sam/bam processing.
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92
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93 The contaminants file parameter was borrowed from the independently developed
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94 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.
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95 Adaption to version 0.11.2 by T. McGowan.
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96
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97 -----
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98
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99 .. class:: infomark
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100
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101 **Inputs and outputs**
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102
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103 FastQC_ is the best place to look for documentation - it's very good.
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104 A summary follows below for those in a tearing hurry.
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105
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106 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
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107 It will also take an optional file containing a list of contaminants information, in the form of
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108 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
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109 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
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110 which modules to include in the output.
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111
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112 The tool produces a basic text and a HTML output file that contain all of the results, including the following:
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113
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114 - Basic Statistics
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115 - Per base sequence quality
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116 - Per sequence quality scores
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117 - Per base sequence content
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118 - Per base GC content
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119 - Per sequence GC content
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120 - Per base N content
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121 - Sequence Length Distribution
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122 - Sequence Duplication Levels
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123 - Overrepresented sequences
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124 - Kmer Content
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125
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126 All except Basic Statistics and Overrepresented sequences are plots.
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127 .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
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128 .. _Picard-tools: http://picard.sourceforge.net/index.shtml
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129 </help>
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130 <citations>
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131 <citation type="bibtex">
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132 @unpublished{andrews_s,
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133 author = {Andrews, S.},
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134 keywords = {bioinformatics, ngs, qc},
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135 priority = {2},
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136 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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137 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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138 }
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139 </citation>
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140 </citations>
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141 </tool>