Mercurial > repos > devteam > fastqc

annotate rgFastQC.xml @ 10:1f6fd7a898bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 4b383d48868d7f3f6d35f242a0ee35953adcb037
author iuc
date Mon, 15 May 2017 08:34:27 -0400
parents 0a7c65540937
children f5a25a56ab9d
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1 <tool id="fastqc" name="FastQC" version="0.68">
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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 '$limits'
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25 #end if
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26 ]]></command>
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27 <inputs>
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28 <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="input_file" type="data"
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29 label="Short read data from your current history" />
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30 <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
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31 help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA" />
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32 <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
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33 help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" />
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34 </inputs>
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35 <outputs>
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36 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
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37 <data format="txt" name="text_file" label="${tool.name} on ${on_string}: RawData" />
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38 </outputs>
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39 <tests>
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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="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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43 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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44 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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45 </test>
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46 <test>
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47 <param name="input_file" value="1000gsample.fastq" />
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48 <param name="limits" value="fastqc_customlimits.txt" ftype="txt" />
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49 <output name="html_file" file="fastqc_report2.html" ftype="html" compare="sim_size" delta="4096"/>
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50 <output name="text_file" file="fastqc_data2.txt" ftype="txt" compare="sim_size"/>
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51 </test>
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52 <test>
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53 <param name="input_file" value="1000gsample.fastq.gz" ftype="fastq.gz" />
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54 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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55 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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56 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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57 </test>
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58 <test>
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59 <param name="input_file" value="1000gsample.fastq.bz2" ftype="fastq.bz2" />
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60 <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" />
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61 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/>
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62 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/>
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63 </test>
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64 </tests>
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65 <help>
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66 .. class:: infomark
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67
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68 **Purpose**
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69
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70 FastQC aims to provide a simple way to do some quality control checks on raw
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71 sequence data coming from high throughput sequencing pipelines.
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72 It provides a modular set of analyses which you can use to give a quick
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73 impression of whether your data has any problems of
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74 which you should be aware before doing any further analysis.
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75
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76 The main functions of FastQC are:
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77
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78 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
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79 - Providing a quick overview to tell you in which areas there may be problems
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80 - Summary graphs and tables to quickly assess your data
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81 - Export of results to an HTML based permanent report
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82 - Offline operation to allow automated generation of reports without running the interactive application
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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 **FastQC**
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89
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90 This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_
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91 Kindly acknowledge it as well as this tool if you use it.
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92 FastQC incorporates the Picard-tools_ libraries for SAM/BAM processing.
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93
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94 The contaminants file parameter was borrowed from the independently developed
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95 fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson.
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96 Adaption to version 0.11.2 by T. McGowan.
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97
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98 -----
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99
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100 .. class:: infomark
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101
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102 **Inputs and outputs**
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103
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104 FastQC_ is the best place to look for documentation - it's very good.
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105 A summary follows below for those in a tearing hurry.
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106
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107 This wrapper will accept a Galaxy fastq, fastq.gz, sam or bam as the input read file to check.
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108 It will also take an optional file containing a list of contaminants information, in the form of
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109 a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom
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110 limits.txt file that allows setting the warning thresholds for the different modules and also specifies
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111 which modules to include in the output.
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112
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113 The tool produces a basic text and a HTML output file that contain all of the results, including the following:
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114
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115 - Basic Statistics
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116 - Per base sequence quality
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117 - Per sequence quality scores
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118 - Per base sequence content
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119 - Per base GC content
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120 - Per sequence GC content
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121 - Per base N content
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122 - Sequence Length Distribution
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123 - Sequence Duplication Levels
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124 - Overrepresented sequences
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125 - Kmer Content
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126
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127 All except Basic Statistics and Overrepresented sequences are plots.
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128 .. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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129 .. _Picard-tools: https://broadinstitute.github.io/picard/
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130 </help>
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131 <citations>
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132 <citation type="bibtex">
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133 @unpublished{andrews_s,
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134 author = {Andrews, S.},
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135 keywords = {bioinformatics, ngs, qc},
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136 priority = {2},
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137 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
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138 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
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139 }
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140 </citation>
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141 </citations>
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142 </tool>